Variant report

Variant	rs9370564
Chromosome Location	chr6:56994024-56994025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56993514..56996955-chr6:57008261..57010355,3	K562	blood:
2	chr6:56903865..56905391-chr6:56992094..56994169,2	K562	blood:
3	chr6:56993831..56996042-chr6:57033956..57036642,2	K562	blood:
4	chr6:56817335..56819913-chr6:56993213..56995240,2	K562	blood:
5	chr6:56986382..56987973-chr6:56993150..56995625,2	K562	blood:
6	chr6:56969351..56971766-chr6:56991775..56994695,2	K562	blood:

Variant related genes	Relation type
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000226803	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1157713	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190434	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192711	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210597	0.93[ASN][1000 genomes]
rs12211611	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2100305	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734738	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778515	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800019	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs3996929	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3996933	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996937	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4715646	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6459180	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6913707	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926980	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6928715	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6929783	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743855	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7744316	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs7744824	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7753537	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753927	0.93[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7763570	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180538	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349843	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367704	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367708	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382680	0.88[YRI][hapmap]
rs9382689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9396259	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952647	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885757	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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 target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9370564	RAB23	cis	cerebellum	SCAN
rs9370564	BEND6	cis	cerebellum	SCAN
rs9370564	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs9370564	ZNF451	cis	cerebellum	SCAN
rs9370564	KIAA1586	cis	cerebellum	SCAN
rs9370564	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs9370564	BEND6	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56966600-57012400	Weak transcription	Spleen	Spleen
2	chr6:56966800-57018000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56967800-56995400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:56967800-56995800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:56968400-57000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:56968600-56998200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:56968600-57002200	Weak transcription	Thymus	Thymus
9	chr6:56968600-57006600	Weak transcription	Brain Angular Gyrus	brain
10	chr6:56968600-57018400	Weak transcription	Psoas Muscle	Psoas
11	chr6:56969200-56995400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:56969200-56997800	Weak transcription	Fetal Lung	lung
13	chr6:56969400-56997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:56969400-56997800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:56969600-56997600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:56969600-56999000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:56970200-57007600	Weak transcription	Fetal Kidney	kidney
18	chr6:56973600-56997000	Weak transcription	NHEK	skin
19	chr6:56973800-56998400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:56974000-57001000	Weak transcription	NH-A	brain
21	chr6:56974000-57012400	Weak transcription	HUVEC	blood vessel
22	chr6:56974200-57012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:56974400-56999600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:56975000-56995400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:56975000-56997800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:56975000-57006400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:56975400-56995200	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:56975400-57006800	Weak transcription	NHLF	lung
29	chr6:56980800-56995600	Weak transcription	NHDF-Ad	bronchial
30	chr6:56982000-56995400	Weak transcription	HSMMtube	muscle
31	chr6:56982400-56997800	Weak transcription	Osteobl	bone
32	chr6:56984000-56998400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:56984200-56995400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:56985600-56998000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:56985600-57036800	Weak transcription	Pancreas	Pancrea
36	chr6:56986000-56998400	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:56986200-56998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:56986400-57012000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:56987800-56997800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:56988000-56995400	Weak transcription	Fetal Stomach	stomach
41	chr6:56988000-56997800	Weak transcription	Fetal Thymus	thymus
42	chr6:56988000-56998400	Weak transcription	Aorta	Aorta
43	chr6:56988000-56998600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:56988000-57009000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:56988200-56994200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:56988200-56996000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:56988200-56997800	Weak transcription	Dnd41	blood
48	chr6:56988200-56998600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:56988200-56999600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:56988200-57009400	Weak transcription	Fetal Intestine Small	intestine

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