Variant report

Variant	rs12056975
Chromosome Location	chr9:101546578-101546579
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101545059..101549166-chr9:101549298..101553118,4	MCF-7	breast:
2	chr9:101546085..101548581-chr9:101557389..101560839,3	MCF-7	breast:
3	chr9:101545621..101549470-chr9:101551390..101554188,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10121153	0.82[EUR][1000 genomes]
rs10760494	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs10819308	0.84[EUR][1000 genomes]
rs10819320	0.82[EUR][1000 genomes]
rs10987747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10987749	0.84[EUR][1000 genomes]
rs10987771	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10987794	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11791440	0.90[EUR][1000 genomes]
rs12057064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12380570	0.93[ASN][1000 genomes]
rs1543506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555519	0.82[EUR][1000 genomes]
rs168083	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs173066	0.86[ASN][1000 genomes]
rs186809	0.92[ASN][1000 genomes]
rs2146255	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337569	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs337572	0.86[ASN][1000 genomes]
rs337577	0.86[ASN][1000 genomes]
rs337578	0.86[ASN][1000 genomes]
rs337581	0.86[ASN][1000 genomes]
rs337591	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs33998698	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889747	0.86[ASN][1000 genomes]
rs3933477	0.91[EUR][1000 genomes]
rs404680	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs420158	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs422531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs450231	0.92[ASN][1000 genomes]
rs4743278	0.87[EUR][1000 genomes]
rs4743281	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs532824	0.86[ASN][1000 genomes]
rs554730	0.95[ASN][1000 genomes]
rs580809	0.82[JPT][hapmap]
rs60698775	0.98[ASN][1000 genomes]
rs7018907	0.81[EUR][1000 genomes]
rs7020056	0.87[EUR][1000 genomes]
rs7027405	0.82[EUR][1000 genomes]
rs7027771	0.88[EUR][1000 genomes]
rs7028766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7035107	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7035722	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7038640	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs7047722	0.88[EUR][1000 genomes]
rs72735324	0.98[ASN][1000 genomes]
rs72735326	0.98[ASN][1000 genomes]
rs7853904	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs7861186	0.81[EUR][1000 genomes]
rs7862858	0.93[ASN][1000 genomes]
rs9886821	0.87[EUR][1000 genomes]
rs9919074	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12056975	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
2	chr9:101496600-101549400	Weak transcription	Small Intestine	intestine
3	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
7	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
8	chr9:101526400-101549400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr9:101530200-101547600	Weak transcription	NHDF-Ad	bronchial
10	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:101533800-101553200	Strong transcription	Fetal Stomach	stomach
12	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
13	chr9:101535600-101553400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:101535800-101552000	Weak transcription	Thymus	Thymus
15	chr9:101535800-101553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:101536000-101553200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
19	chr9:101536200-101553400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
21	chr9:101536800-101551400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:101536800-101551600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr9:101537000-101557400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:101537400-101547000	Genic enhancers	Fetal Intestine Small	intestine
25	chr9:101537600-101549800	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:101538200-101553000	Weak transcription	NH-A	brain
27	chr9:101538800-101552400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:101539000-101546600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:101539000-101553000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:101540400-101546600	Strong transcription	Pancreas	Pancrea
31	chr9:101541600-101547800	Weak transcription	Gastric	stomach
32	chr9:101541600-101553000	Weak transcription	Brain Anterior Caudate	brain
33	chr9:101542000-101553200	Weak transcription	HUVEC	blood vessel
34	chr9:101542400-101546800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr9:101542600-101548000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:101542600-101548000	Weak transcription	Fetal Thymus	thymus
37	chr9:101542600-101553200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:101542800-101547200	Strong transcription	Primary T cells from cord blood	blood
39	chr9:101543200-101546600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:101543200-101547000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:101543400-101546600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:101543400-101546800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr9:101543400-101546800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:101543400-101546800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:101543400-101547000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:101543600-101546600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:101543600-101546600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:101543600-101546600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:101543600-101546600	Strong transcription	Brain Angular Gyrus	brain
50	chr9:101543600-101546600	Strong transcription	Brain Inferior Temporal Lobe	brain

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