Variant report

Variant	rs2624842
Chromosome Location	chr3:50196418-50196419
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:50196300-50196450	HCM	heart:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
2	RCOR1	chr3:50196110-50196636	IMR90	lung:	n/a	n/a
3	CTCF	chr3:50196280-50196430	HRPEpiC	eye:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
4	CTCF	chr3:50196300-50196450	HFF-Myc	foreskin:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
5	CTCF	chr3:50196320-50196470	HUVEC	blood vessel:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
6	CTCF	chr3:50196300-50196450	Hela-S3	cervix:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
7	CTCF	chr3:50196380-50196530	HAc	cerebellar:	n/a	n/a
8	RCOR1	chr3:50196269-50196493	K562	blood:	n/a	n/a
9	CTCF	chr3:50196300-50196450	HEEpiC	esophagus:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
10	CTCF	chr3:50196279-50196433	HUVEC	blood vessel:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
11	CTCF	chr3:50196360-50196510	MCF-7	breast:	n/a	n/a
12	CTCF	chr3:50196280-50196430	SAEC	small airway:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
13	CTCF	chr3:50196280-50196430	HMEC	breast:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
14	CTCF	chr3:50196300-50196450	HepG2	liver:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
15	RCOR1	chr3:50196232-50196496	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr3:50196280-50196430	HUVEC	blood vessel:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
17	CTCF	chr3:50196300-50196450	NHEK	skin:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
18	POLR2A	chr3:50195264-50196721	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr3:50196320-50196470	RPTEC	kidney:	n/a	chr3:50196322-50196343 chr3:50196327-50196345
20	ZNF143	chr3:50196312-50196443	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:50196233-50196438	NHEK	skin:	n/a	chr3:50196322-50196343 chr3:50196327-50196345 chr3:50196239-50196247
22	CTCF	chr3:50196340-50196490	HPF	lung:	n/a	n/a
23	STAT3	chr3:50196370-50196560	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr3:50196280-50196430	HPF	lung:	n/a	chr3:50196322-50196343 chr3:50196327-50196345

No.	Distal block	Cell Line	Cell type
1	chr3:50190470..50194491-chr3:50196225..50201802,7	K562	blood:
2	chr3:50194714..50196531-chr3:50230211..50232377,2	K562	blood:
3	chr3:50192650..50196663-chr3:50219720..50222472,4	MCF-7	breast:
4	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235016	TF binding region
SEMA3F	TF binding region
ENSG00000235016	Chromatin interaction
ENSG00000114349	Chromatin interaction
ENSG00000207922	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10510755	0.95[GIH][hapmap]
rs1061474	0.89[JPT][hapmap]
rs1138536	0.89[JPT][hapmap]
rs12629572	0.86[GIH][hapmap]
rs12631337	0.91[ASN][1000 genomes]
rs1989839	0.86[GIH][hapmap]
rs2073498	0.90[GIH][hapmap]
rs2236939	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap]
rs2301639	0.95[GIH][hapmap]
rs2526392	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs2526393	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2526394	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2526395	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs2526396	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs2526400	0.97[ASN][1000 genomes]
rs2624826	0.89[JPT][hapmap]
rs2624836	0.99[ASN][1000 genomes]
rs2624837	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs2624840	0.93[ASN][1000 genomes]
rs28365992	0.90[GIH][hapmap]
rs2856237	0.89[JPT][hapmap]
rs2856238	0.89[JPT][hapmap]
rs2859580	0.81[ASN][1000 genomes]
rs3806708	0.90[GIH][hapmap]
rs57462170	0.90[ASN][1000 genomes]
rs57842657	0.99[ASN][1000 genomes]
rs6446201	0.96[ASN][1000 genomes]
rs6446202	0.85[CEU][hapmap];0.85[ASN][1000 genomes]
rs6776145	0.86[GIH][hapmap]
rs739431	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs7642692	0.85[CEU][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2624842	DALRD3	cis	parietal	SCAN
rs2624842	NEK4	cis	parietal	SCAN
rs2624842	SFMBT1	cis	parietal	SCAN
rs2624842	ARIH2	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50193600-50197800	Weak transcription	Fetal Heart	heart
2	chr3:50193600-50197800	Weak transcription	Small Intestine	intestine
3	chr3:50194200-50203800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:50194200-50208800	Weak transcription	Pancreas	Pancrea
5	chr3:50194400-50197000	Flanking Active TSS	HMEC	breast
6	chr3:50194400-50197800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:50194400-50199000	Enhancers	Stomach Mucosa	stomach
8	chr3:50194400-50201000	Weak transcription	Psoas Muscle	Psoas
9	chr3:50194600-50199000	Enhancers	Fetal Brain Male	brain
10	chr3:50194800-50196600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:50194800-50196600	Enhancers	Right Atrium	heart
12	chr3:50194800-50196800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:50194800-50196800	Bivalent Enhancer	Fetal Intestine Small	intestine
14	chr3:50194800-50196800	Enhancers	Fetal Muscle Leg	muscle
15	chr3:50194800-50197200	Enhancers	K562	blood
16	chr3:50194800-50200800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:50194800-50200800	Enhancers	Colon Smooth Muscle	Colon
18	chr3:50194800-50200800	Weak transcription	NHDF-Ad	bronchial
19	chr3:50194800-50202600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:50194800-50207600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr3:50195000-50196600	Enhancers	Right Ventricle	heart
22	chr3:50195000-50196800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:50195000-50196800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:50195000-50196800	Enhancers	A549	lung
25	chr3:50195000-50197000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:50195000-50197000	Enhancers	Fetal Thymus	thymus
27	chr3:50195000-50197200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:50195000-50197400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:50195000-50197800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:50195000-50198000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:50195000-50198200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:50195000-50198400	Enhancers	HUVEC	blood vessel
33	chr3:50195000-50201200	Enhancers	Adipose Nuclei	Adipose
34	chr3:50195200-50196600	Enhancers	HepG2	liver
35	chr3:50195200-50197000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:50195200-50197200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:50195200-50199000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:50195400-50196800	Enhancers	Brain Cingulate Gyrus	brain
39	chr3:50195400-50197200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:50195400-50210200	Genic enhancers	Fetal Stomach	stomach
41	chr3:50195400-50210600	Enhancers	Left Ventricle	heart
42	chr3:50195400-50210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:50195600-50197400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:50195600-50197800	Weak transcription	Colonic Mucosa	Colon
45	chr3:50195600-50198800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:50195600-50200400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:50195800-50196600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:50195800-50196800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:50195800-50196800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:50195800-50197000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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