Variant report

Variant	rs739431
Chromosome Location	chr3:50255305-50255306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50255255-50255786	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:50254925-50255912	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:50255295-50255345	NT2-D1	testis:	n/a
2	chr3:50255295-50255345	NHBE	bronchial:	n/a
3	chr3:50255295-50255345	AG04449	skin:	fetal
4	chr3:50255295-50255345	AG09319	gingival:	n/a
5	chr3:50255295-50255345	HepG2	liver:	n/a
6	chr3:50255295-50255345	GM12878	blood:	n/a
7	chr3:50255295-50255345	SKMC	muscle:	n/a
8	chr3:50255295-50255345	GM12891	blood:	n/a
9	chr3:50255295-50255345	HEK293	kidney:	embryo
10	chr3:50255295-50255345	PANC-1	pancreas:	n/a
11	chr3:50255295-50255345	NB4	blood:	n/a
12	chr3:50255295-50255345	CMK	blood:	n/a
13	chr3:50255295-50255345	HUVEC	blood vessel:	n/a
14	chr3:50255295-50255345	A549	lung:	n/a
15	chr3:50255295-50255345	RPTEC	kidney:	n/a
16	chr3:50255295-50255345	HCT-116	colon:	n/a
17	chr3:50255295-50255345	GM12892	blood:	n/a
18	chr3:50255295-50255345	PFSK-1	brain:	n/a
19	chr3:50255295-50255345	HMEC	breast:	n/a
20	chr3:50255295-50255345	NHDF-neo	bronchial:	n/a
21	chr3:50255295-50255345	AG10803	skin:	n/a
22	chr3:50255295-50255345	K562	blood:	n/a
23	chr3:50255295-50255345	BE2_C	brain:	n/a
24	chr3:50255295-50255345	HCM	heart:	n/a
25	chr3:50255295-50255345	T-47D	breast:	n/a
26	chr3:50255295-50255345	AG04450	lung:	fetal
27	chr3:50255295-50255345	AoSMC	blood vessel:	n/a
28	chr3:50255295-50255345	ECC-1	luminal epithelium:	n/a
29	chr3:50255295-50255345	GM06990	blood:	n/a
30	chr3:50255295-50255345	ProgFib	skin:	n/a
31	chr3:50255295-50255345	HPAEpiC	pulmonary alveolar:	n/a
32	chr3:50255295-50255345	U87	brain:	n/a
33	chr3:50255295-50255345	HCPEpiC	choroid plexus:	n/a
34	chr3:50255295-50255345	Caco-2	colon:	n/a
35	chr3:50255295-50255345	MCF10A-Er-Src	breast:	n/a
36	chr3:50255295-50255345	SK-N-SH	brain:	n/a
37	chr3:50255295-50255345	NH-A	brain:	n/a
38	chr3:50255295-50255345	Jurkat	blood:	n/a
39	chr3:50255295-50255345	HRCEpiC	kidney:	n/a
40	chr3:50255295-50255345	HEEpiC	esophagus:	n/a
41	chr3:50255295-50255345	HRE	kidney:	n/a
42	chr3:50255295-50255345	HRPEpiC	eye:	n/a
43	chr3:50255295-50255345	SK-N-MC	brain:	n/a
44	chr3:50255295-50255345	BJ	skin:	n/a
45	chr3:50255295-50255345	PrEC	prostate:	n/a
46	chr3:50255295-50255345	HL-60	blood:	n/a
47	chr3:50255295-50255345	HIPEpiC	eye:	n/a
48	chr3:50255295-50255345	HCF	heart:	n/a
49	chr3:50255295-50255345	H1-hESC	embryonic stem cell:	embryo
50	chr3:50255295-50255345	SK-N-SH_RA	brain:	n/a

No data

Variant related genes	Relation type
SLC38A3	TF binding region
SLC38A3	CpG island

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs2013208	0.82[JPT][hapmap]
rs2073499	0.87[CEU][hapmap];0.96[GIH][hapmap]
rs2233474	0.87[CEU][hapmap];0.96[GIH][hapmap]
rs2236939	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2236951	0.81[GIH][hapmap]
rs2240326	0.82[JPT][hapmap]
rs2240327	0.82[JPT][hapmap]
rs2240329	0.82[JPT][hapmap]
rs2282751	0.96[GIH][hapmap]
rs2301166	0.90[JPT][hapmap]
rs2526392	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2526393	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs2526394	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2526395	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2526396	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2526748	0.82[JPT][hapmap]
rs2526751	0.82[JPT][hapmap]
rs2526754	0.82[JPT][hapmap]
rs2624837	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2624842	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2624847	0.82[JPT][hapmap]
rs2624853	0.82[JPT][hapmap]
rs2856234	0.90[JPT][hapmap]
rs4141060	0.87[CEU][hapmap];0.96[GIH][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4688755	0.82[JPT][hapmap]
rs57462170	0.82[ASN][1000 genomes]
rs6446193	0.82[JPT][hapmap]
rs6446202	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7621352	0.82[JPT][hapmap]
rs7642692	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9311446	0.82[JPT][hapmap]
rs9814664	0.82[JPT][hapmap]
rs9861216	0.82[JPT][hapmap]
rs9866695	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
10	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
11	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
14	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
15	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
24	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
25	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
26	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
28	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
29	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
30	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
31	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs739431	DALRD3	cis	parietal	SCAN
rs739431	PCBP4	cis	parietal	SCAN
rs739431	TRAIP	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50244000-50263800	Weak transcription	Right Atrium	heart
2	chr3:50244200-50263800	Weak transcription	Left Ventricle	heart
3	chr3:50244400-50263800	Weak transcription	Right Ventricle	heart
4	chr3:50247400-50264400	Weak transcription	Ovary	ovary
5	chr3:50249000-50259000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:50250000-50256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:50250200-50255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:50250600-50255800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:50251400-50257800	Genic enhancers	Liver	Liver
10	chr3:50251600-50257400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:50251600-50263600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:50251800-50257400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:50251800-50263400	Weak transcription	Fetal Brain Female	brain
14	chr3:50251800-50263800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:50252000-50257200	Strong transcription	HepG2	liver
16	chr3:50252200-50256000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:50252800-50255600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:50252800-50257600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:50253000-50255800	Strong transcription	Pancreas	Pancrea
20	chr3:50253000-50257600	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:50253000-50260000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:50253800-50257400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:50254000-50255600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:50254000-50257800	Strong transcription	Fetal Stomach	stomach
25	chr3:50254600-50255600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:50254600-50256000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:50254600-50256200	Enhancers	Esophagus	oesophagus
28	chr3:50254600-50256600	Strong transcription	Brain Cingulate Gyrus	brain
29	chr3:50254600-50257200	Strong transcription	Brain Hippocampus Middle	brain
30	chr3:50254600-50257800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:50254800-50255600	Enhancers	NHEK	skin
32	chr3:50254800-50256000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:50255000-50255400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:50255000-50255400	Enhancers	HMEC	breast
35	chr3:50255000-50256200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:50255000-50256200	Weak transcription	Psoas Muscle	Psoas
37	chr3:50255000-50257400	Strong transcription	Brain Substantia Nigra	brain
38	chr3:50255200-50255400	Enhancers	Spleen	Spleen
39	chr3:50255200-50256200	Active TSS	Gastric	stomach

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