Variant report

Variant	rs7938790
Chromosome Location	chr11:102160633-102160634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102159577..102161091-chr11:102161248..102163648,2	MCF-7	breast:
2	chr11:102159539..102162483-chr11:102186552..102188532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023445	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10501998	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10501999	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225201	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225202	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225203	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11600522	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11602147	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11606268	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12098902	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12280343	0.93[ASN][1000 genomes]
rs12576911	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12787745	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12789170	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12794196	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17763827	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17763887	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17769417	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17878708	0.89[ASN][1000 genomes]
rs1894113	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894114	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894115	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408344	0.83[ASN][1000 genomes]
rs2511293	0.92[ASN][1000 genomes]
rs2511295	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2604526	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2604527	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2604533	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2846848	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2846849	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2846857	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2846858	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2852879	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2852880	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2852881	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2852882	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2852891	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132831	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35612369	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58277500	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61893629	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7480738	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924744	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928663	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7931341	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9665961	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7938790	BIRC3	cis	Adipose Subcutaneous	GTEx
rs7938790	C11orf70	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102157800-102161000	Enhancers	Stomach Mucosa	stomach
2	chr11:102159000-102161200	Enhancers	Fetal Stomach	stomach
3	chr11:102159000-102161600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:102159200-102160800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:102159200-102160800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:102159200-102161000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:102159200-102161000	Enhancers	Colon Smooth Muscle	Colon
8	chr11:102159200-102161000	Enhancers	Fetal Lung	lung
9	chr11:102159200-102161000	Enhancers	Hela-S3	cervix
10	chr11:102159200-102161200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:102159200-102161600	Enhancers	Dnd41	blood
12	chr11:102159200-102162000	Enhancers	Fetal Thymus	thymus
13	chr11:102159200-102163600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:102159200-102163800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:102159200-102164600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:102159200-102164600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:102159200-102164600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr11:102159200-102165000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:102159200-102165800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:102159400-102161000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:102159400-102161600	Enhancers	Primary B cells from peripheral blood	blood
22	chr11:102159400-102162800	Enhancers	Thymus	Thymus
23	chr11:102159400-102163800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:102159400-102163800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:102159400-102164000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:102159400-102164200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:102159400-102164200	Weak transcription	GM12878-XiMat	blood
28	chr11:102159600-102160800	Enhancers	Primary B cells from cord blood	blood
29	chr11:102159600-102161400	Weak transcription	K562	blood
30	chr11:102159600-102161600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:102159600-102163800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:102159600-102164400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:102159600-102164800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:102159800-102161000	Enhancers	HepG2	liver
35	chr11:102159800-102163800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:102160000-102161000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:102160000-102161000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:102160000-102161000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:102160000-102161000	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr11:102160200-102160800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr11:102160200-102160800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr11:102160200-102160800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:102160200-102160800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:102160200-102160800	Enhancers	Adipose Nuclei	Adipose
45	chr11:102160200-102160800	Enhancers	NHDF-Ad	bronchial
46	chr11:102160200-102160800	Enhancers	Osteobl	bone
47	chr11:102160200-102161000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:102160200-102161000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:102160200-102161000	Enhancers	HMEC	breast
50	chr11:102160400-102160800	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links