Variant report

Variant	rs2518796
Chromosome Location	chr3:50207075-50207076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50205683-50207219	HUVEC	blood vessel:	n/a	n/a
2	GTF2F1	chr3:50207039-50207167	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr3:50206919-50207182	Hela-S3	cervix:	n/a	chr3:50207087-50207097
4	CHD2	chr3:50206851-50207146	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50194586..50199661-chr3:50206741..50210376,5	K562	blood:
2	chr3:50201604..50203963-chr3:50205181..50207693,2	K562	blood:
3	chr3:50205468..50208057-chr3:50211488..50214653,3	K562	blood:
4	chr3:50202263..50203963-chr3:50204980..50207693,2	K562	blood:
5	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:
6	chr3:50206530..50208050-chr3:50212399..50214465,2	K562	blood:

No data

Variant related genes	Relation type
MIR566	TF binding region
SEMA3F	TF binding region
ENSG00000235016	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1005678	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11130230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130237	1.00[JPT][hapmap]
rs11130240	1.00[JPT][hapmap]
rs11916261	1.00[JPT][hapmap]
rs11916999	1.00[JPT][hapmap]
rs11919418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11920034	1.00[JPT][hapmap]
rs11924670	1.00[JPT][hapmap]
rs11924711	1.00[JPT][hapmap]
rs12490944	1.00[JPT][hapmap]
rs12495114	1.00[JPT][hapmap]
rs12629129	1.00[JPT][hapmap]
rs12629553	1.00[JPT][hapmap]
rs12631192	1.00[JPT][hapmap]
rs12631248	1.00[JPT][hapmap]
rs12636232	1.00[JPT][hapmap]
rs12636449	0.82[ASN][1000 genomes]
rs12637457	1.00[JPT][hapmap]
rs12639175	1.00[JPT][hapmap]
rs2023952	1.00[JPT][hapmap]
rs2188151	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518795	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526389	0.89[EUR][1000 genomes]
rs2624833	0.81[AMR][1000 genomes]
rs2624839	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes]
rs2624841	0.88[AMR][1000 genomes]
rs60429865	0.91[ASN][1000 genomes]
rs6800021	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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
26	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
27	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
28	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2518796	GNL3	cis	cerebellum	SCAN
rs2518796	RNF123	cis	parietal	SCAN
rs2518796	RBM6	cis	multi-tissue	Pritchard
rs2518796	RBM6	cis	cerebellum	SCAN
rs2518796	PTH1R	cis	parietal	SCAN
rs2518796	RBM6	cis	Whole Blood	GTEx
rs2518796	RNF123	cis	cerebellum	SCAN
rs2518796	HYAL3	cis	multi-tissue	Pritchard
rs2518796	GNL3	cis	parietal	SCAN
rs2518796	RBM6	cis	parietal	SCAN
rs2518796	RBM6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50194200-50208800	Weak transcription	Pancreas	Pancrea
2	chr3:50194800-50207600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
3	chr3:50195400-50210200	Genic enhancers	Fetal Stomach	stomach
4	chr3:50195400-50210600	Enhancers	Left Ventricle	heart
5	chr3:50195400-50210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:50196200-50211600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:50197200-50211600	Genic enhancers	Esophagus	oesophagus
8	chr3:50197800-50207600	Enhancers	Colonic Mucosa	Colon
9	chr3:50199200-50209400	Enhancers	Placenta	Placenta
10	chr3:50200000-50209600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:50200000-50210400	Enhancers	Fetal Brain Male	brain
12	chr3:50200600-50211800	Enhancers	Right Ventricle	heart
13	chr3:50201800-50207400	Enhancers	Brain Hippocampus Middle	brain
14	chr3:50202000-50207200	Enhancers	Small Intestine	intestine
15	chr3:50202000-50210600	Enhancers	A549	lung
16	chr3:50202200-50210400	Enhancers	Lung	lung
17	chr3:50202400-50208800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:50202800-50207200	Enhancers	Fetal Lung	lung
19	chr3:50202800-50211000	Enhancers	Fetal Muscle Leg	muscle
20	chr3:50203000-50210000	Enhancers	Duodenum Mucosa	Duodenum
21	chr3:50203400-50211400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:50203800-50210000	Genic enhancers	HMEC	breast
23	chr3:50204000-50207200	Enhancers	Colon Smooth Muscle	Colon
24	chr3:50204000-50208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:50204000-50208200	Weak transcription	Fetal Heart	heart
26	chr3:50204000-50208400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:50204000-50208800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:50204200-50207800	Enhancers	Adipose Nuclei	Adipose
29	chr3:50204200-50208200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:50204200-50208200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:50204200-50208400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:50204400-50211000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:50204600-50209600	Enhancers	HUVEC	blood vessel
34	chr3:50204600-50226600	Weak transcription	Brain Anterior Caudate	brain
35	chr3:50204800-50207800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:50204800-50208200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:50204800-50208400	Weak transcription	Liver	Liver
38	chr3:50204800-50208600	Weak transcription	Psoas Muscle	Psoas
39	chr3:50204800-50210400	Enhancers	Stomach Smooth Muscle	stomach
40	chr3:50204800-50210600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:50204800-50211200	Weak transcription	Aorta	Aorta
42	chr3:50204800-50211800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:50205000-50208600	Enhancers	HepG2	liver
44	chr3:50205000-50209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:50205000-50212800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:50205200-50208800	Flanking Active TSS	Hela-S3	cervix
47	chr3:50205400-50207600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:50205400-50208000	Weak transcription	NH-A	brain
49	chr3:50205400-50208200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:50205400-50208200	Weak transcription	HSMM	muscle

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