Variant report

Variant	rs4777740
Chromosome Location	chr15:93389910-93389911
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93388979..93392872-chr15:93411165..93413494,3	MCF-7	breast:
2	chr15:93362035..93364370-chr15:93388613..93390406,2	K562	blood:
3	chr15:93380616..93384575-chr15:93388777..93392228,3	MCF-7	breast:
4	chr15:93388546..93390834-chr15:93426060..93428356,2	MCF-7	breast:
5	chr15:93361450..93364004-chr15:93388773..93390395,2	MCF-7	breast:
6	chr15:93387429..93390014-chrX:12996770..12998336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272888	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11074108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11074109	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11074110	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11074111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28360722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613292	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28734059	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28880667	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4408491	0.85[EUR][1000 genomes]
rs4628913	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4777741	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4777742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778045	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6496994	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7180599	0.89[ASN][1000 genomes]
rs7181781	0.94[ASN][1000 genomes]
rs7184028	0.87[CEU][hapmap];0.93[CHB][hapmap];0.88[EUR][1000 genomes]
rs8023522	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8026478	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027176	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8027321	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8028071	0.90[AMR][1000 genomes]
rs8029902	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030383	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8031154	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8031163	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93383400-93390400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:93383800-93396600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:93384000-93394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:93384800-93391800	Weak transcription	Placenta	Placenta
5	chr15:93386200-93390600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:93386600-93390600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:93386800-93393800	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:93387400-93391600	Weak transcription	Spleen	Spleen
9	chr15:93388000-93390000	Enhancers	Hela-S3	cervix
10	chr15:93388000-93390200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:93388000-93393000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:93388200-93390400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:93388200-93392600	Enhancers	NHDF-Ad	bronchial
14	chr15:93388400-93390400	Weak transcription	Fetal Intestine Large	intestine
15	chr15:93388400-93390400	Enhancers	Osteobl	bone
16	chr15:93388400-93390600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:93388600-93390600	Enhancers	HepG2	liver
18	chr15:93388600-93391200	Weak transcription	HSMM	muscle
19	chr15:93388600-93392200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr15:93388600-93393200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr15:93388600-93393600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr15:93388600-93393600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr15:93388800-93390000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:93388800-93390400	Enhancers	A549	lung
25	chr15:93388800-93390400	Weak transcription	NHLF	lung
26	chr15:93388800-93390800	Weak transcription	K562	blood
27	chr15:93388800-93391000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr15:93388800-93391200	Weak transcription	NH-A	brain
29	chr15:93388800-93392200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr15:93388800-93393600	Enhancers	Primary B cells from cord blood	blood
31	chr15:93388800-93393600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:93388800-93393600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:93389000-93390400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr15:93389000-93391800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:93389000-93392400	Enhancers	Primary T cells from cord blood	blood
36	chr15:93389000-93393600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr15:93389400-93390000	Enhancers	Dnd41	blood
38	chr15:93389400-93390000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr15:93389400-93390800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:93389400-93391600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:93389400-93391800	Weak transcription	Lung	lung
42	chr15:93389400-93392000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:93389400-93392200	Weak transcription	Thymus	Thymus
44	chr15:93389600-93390000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:93389600-93391400	Weak transcription	Fetal Thymus	thymus
46	chr15:93389600-93391600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:93389600-93391600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:93389600-93391800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:93389600-93392800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:93389800-93390000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links