Variant report

Variant	rs3766916
Chromosome Location	chr1:155049402-155049403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154981203..154983632-chr1:155047843..155050809,2	MCF-7	breast:
2	chr1:155048313..155050374-chr1:155107968..155109802,2	K562	blood:
3	chr1:155011198..155013215-chr1:155047880..155049655,2	MCF-7	breast:
4	chr1:154966527..154969835-chr1:155047829..155051093,3	MCF-7	breast:
5	chr1:155048313..155051843-chr1:155107968..155110316,3	K562	blood:
6	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:
7	chr1:154929943..154932868-chr1:155047955..155049522,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232093	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1001848	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10157801	0.85[JPT][hapmap]
rs10908454	1.00[JPT][hapmap]
rs10908455	1.00[JPT][hapmap]
rs10908456	1.00[JPT][hapmap]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11264306	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11264307	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11264314	1.00[JPT][hapmap]
rs11264319	1.00[JPT][hapmap]
rs11264329	1.00[JPT][hapmap]
rs12025371	0.85[JPT][hapmap]
rs12028043	0.85[JPT][hapmap]
rs12040970	1.00[JPT][hapmap]
rs12047986	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12145362	1.00[JPT][hapmap]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[JPT][hapmap]
rs1564124	0.89[ASN][1000 genomes]
rs1870939	1.00[JPT][hapmap]
rs2306124	1.00[JPT][hapmap]
rs35902694	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3765087	1.00[JPT][hapmap]
rs3806256	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4045192	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[JPT][hapmap]
rs4845712	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs6427158	1.00[JPT][hapmap]
rs6665822	1.00[JPT][hapmap]
rs6693477	1.00[JPT][hapmap]
rs7364524	0.85[JPT][hapmap]
rs7365544	1.00[JPT][hapmap]
rs7367207	1.00[JPT][hapmap]
rs7367897	1.00[JPT][hapmap]
rs7368345	1.00[JPT][hapmap]
rs7534162	1.00[JPT][hapmap]
rs7548955	1.00[JPT][hapmap]
rs9297	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS 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	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised 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	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3766916	RPRD2	cis	parietal	SCAN
rs3766916	EFNA1	cis	cerebellum	SCAN
rs3766916	ADAM15	cis	lymphoblastoid	seeQTL
rs3766916	CRNN	cis	cerebellum	SCAN
rs3766916	RORC	cis	cerebellum	SCAN
rs3766916	APOA1BP	cis	cerebellum	SCAN
rs3766916	S100A3	cis	parietal	SCAN
rs3766916	SMCP	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155043800-155050800	Weak transcription	A549	lung
2	chr1:155044000-155051000	Weak transcription	Pancreas	Pancrea
3	chr1:155044000-155051000	Weak transcription	Right Atrium	heart
4	chr1:155044200-155050000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:155044200-155050800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:155044600-155050600	Weak transcription	Spleen	Spleen
7	chr1:155044600-155050800	Weak transcription	Lung	lung
8	chr1:155044600-155051000	Weak transcription	Gastric	stomach
9	chr1:155044800-155050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:155046400-155049600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:155046400-155050000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:155046400-155050600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:155046400-155051000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:155046400-155051000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:155046600-155049800	Weak transcription	HMEC	breast
16	chr1:155046600-155050000	Weak transcription	Esophagus	oesophagus
17	chr1:155046600-155050000	Weak transcription	NHEK	skin
18	chr1:155046600-155050400	Enhancers	Primary T cells from cord blood	blood
19	chr1:155046600-155050600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:155046600-155050600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:155046600-155050800	Weak transcription	GM12878-XiMat	blood
22	chr1:155046600-155051000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:155046600-155051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:155046800-155050600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:155046800-155050800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:155046800-155051000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:155047200-155050800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:155047200-155051000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:155047400-155050000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:155047400-155050800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:155047800-155050800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:155047800-155050800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:155048200-155050000	Enhancers	K562	blood
34	chr1:155048800-155050000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:155048800-155051400	Bivalent Enhancer	Fetal Thymus	thymus
36	chr1:155049200-155050800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links