Variant report

Variant	rs2968853
Chromosome Location	chr7:150639871-150639872
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	chr7:150638034..150640570-chr7:150647564..150649196,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1137617	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12540183	0.86[EUR][1000 genomes]
rs13244889	0.86[EUR][1000 genomes]
rs2907947	0.82[EUR][1000 genomes]
rs2968855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968857	0.96[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2968860	0.85[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2968862	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4725384	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4725980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725983	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs731724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs882156	0.92[GIH][hapmap];0.90[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs887586	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2758140	chr7:150538821-150663697	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759574	chr7:150538821-150663697	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
8	nsv465212	chr7:150598492-150667210	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv609000	chr7:150598492-150667210	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv465213	chr7:150606288-150667210	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv609001	chr7:150606288-150667210	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1022246	chr7:150619660-150779924	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2968853	TMEM176B	cis	cerebellum	SCAN
rs2968853	ZNF786	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150634400-150640400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:150634400-150643800	Enhancers	HMEC	breast
3	chr7:150634800-150643600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:150635000-150644400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:150635600-150642400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:150635600-150642600	Weak transcription	Brain Anterior Caudate	brain
7	chr7:150635600-150648000	Weak transcription	Ovary	ovary
8	chr7:150637000-150642000	Weak transcription	Fetal Brain Female	brain
9	chr7:150637200-150641200	Enhancers	Fetal Heart	heart
10	chr7:150637800-150640400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:150637800-150642400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:150637800-150652400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:150638000-150641600	Weak transcription	Fetal Intestine Small	intestine
14	chr7:150638000-150642000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:150638400-150640000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:150638400-150640200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr7:150638400-150640600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:150638600-150640000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:150638600-150640000	Enhancers	NHEK	skin
20	chr7:150638600-150640200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:150638600-150640200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr7:150638600-150640400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:150638600-150640400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr7:150638600-150640400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:150638600-150640400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr7:150638600-150640600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:150638600-150640600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr7:150638600-150640600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr7:150638600-150640800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr7:150638600-150641800	Enhancers	Esophagus	oesophagus
31	chr7:150638600-150642200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:150638800-150640000	Enhancers	Colon Smooth Muscle	Colon
33	chr7:150638800-150640200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr7:150638800-150640200	Enhancers	Thymus	Thymus
35	chr7:150638800-150640400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:150638800-150640400	Enhancers	Left Ventricle	heart
37	chr7:150638800-150643400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr7:150639000-150640000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr7:150639000-150640000	Enhancers	Fetal Brain Male	brain
40	chr7:150639000-150640000	Enhancers	K562	blood
41	chr7:150639000-150640200	Enhancers	Primary hematopoietic stem cells	blood
42	chr7:150639000-150640400	Enhancers	Right Ventricle	heart
43	chr7:150639200-150640000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr7:150639200-150640000	Enhancers	Spleen	Spleen
45	chr7:150639400-150643400	Enhancers	Fetal Intestine Large	intestine
46	chr7:150639600-150640200	Enhancers	Fetal Stomach	stomach
47	chr7:150639600-150640600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr7:150639600-150642200	Weak transcription	Fetal Lung	lung
49	chr7:150639600-150642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr7:150639600-150650800	Weak transcription	Pancreas	Pancrea

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