Variant report

Variant	rs10947432
Chromosome Location	chr6:33676556-33676557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33673686..33677249-chr6:33690275..33693823,3	K562	blood:
2	chr6:33676238..33679184-chr6:33722714..33724604,2	MCF-7	breast:
3	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:
4	chr6:33674390..33676592-chr6:34040123..34042729,2	MCF-7	breast:
5	chr6:33674734..33677061-chr6:34117510..34119427,2	K562	blood:
6	chr6:33554633..33558061-chr6:33675915..33678804,3	MCF-7	breast:
7	chr6:33545816..33547496-chr6:33675270..33677360,2	K562	blood:
8	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266509	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000197251	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10456075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947415	0.84[CEU][hapmap]
rs10947427	0.83[GIH][hapmap]
rs10947441	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs11757379	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12189725	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12190155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193658	0.81[EUR][1000 genomes]
rs12195707	0.84[CEU][hapmap]
rs12199132	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205398	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12207382	0.85[JPT][hapmap]
rs12211490	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs12211554	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12211565	0.82[ASN][1000 genomes]
rs12214669	1.00[LWK][hapmap]
rs12215329	0.82[ASN][1000 genomes]
rs12660955	0.82[ASN][1000 genomes]
rs12661400	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12662447	0.81[EUR][1000 genomes]
rs13200063	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13203745	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13204162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13204975	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13206228	0.82[ASN][1000 genomes]
rs13207666	0.91[ASN][1000 genomes]
rs13214874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274459	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2281831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281917	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281918	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296737	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296749	0.82[ASN][1000 genomes]
rs34139049	0.88[ASN][1000 genomes]
rs34339105	0.82[ASN][1000 genomes]
rs34472165	0.82[ASN][1000 genomes]
rs34778247	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34869648	0.82[ASN][1000 genomes]
rs35095444	0.89[EUR][1000 genomes]
rs35274562	0.88[ASN][1000 genomes]
rs35646598	0.88[ASN][1000 genomes]
rs35698850	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35721478	0.82[ASN][1000 genomes]
rs35797388	0.82[ASN][1000 genomes]
rs3793080	0.80[TSI][hapmap]
rs3806107	0.80[TSI][hapmap]
rs3818526	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4559081	1.00[LWK][hapmap]
rs66670017	0.82[ASN][1000 genomes]
rs68168863	0.82[ASN][1000 genomes]
rs6925337	0.85[JPT][hapmap]
rs729376	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751095	0.82[ASN][1000 genomes]
rs755239	0.82[ASN][1000 genomes]
rs877187	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296097	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9469554	0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10947432	C6orf125	cis	cerebellum	SCAN
rs10947432	LEMD2	cis	parietal	SCAN
rs10947432	ITPR3	cis	multi-tissue	Pritchard
rs10947432	LEMD2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
2	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
3	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
6	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
7	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
8	chr6:33665600-33678200	Weak transcription	NH-A	brain
9	chr6:33665600-33678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:33665800-33676600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:33666000-33676600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:33666000-33677800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:33666000-33678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:33666200-33677600	Weak transcription	Psoas Muscle	Psoas
15	chr6:33666400-33677800	Weak transcription	Brain Anterior Caudate	brain
16	chr6:33666600-33677800	Weak transcription	Right Atrium	heart
17	chr6:33666600-33678200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:33666600-33678400	Weak transcription	Colonic Mucosa	Colon
19	chr6:33666600-33678400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:33667000-33678400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:33667200-33676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:33668400-33677800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:33668600-33677800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:33668600-33677800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:33668600-33678000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:33668600-33678200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:33668600-33678200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:33669200-33677800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:33669600-33676600	Weak transcription	Hela-S3	cervix
30	chr6:33670400-33676600	Strong transcription	Fetal Muscle Leg	muscle
31	chr6:33670400-33677800	Weak transcription	HSMMtube	muscle
32	chr6:33670400-33678000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:33670800-33678200	Weak transcription	NHDF-Ad	bronchial
34	chr6:33671400-33677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:33672000-33677400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:33672200-33677600	Strong transcription	Thymus	Thymus
37	chr6:33672600-33676800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr6:33672600-33678000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:33673200-33676800	Enhancers	Fetal Brain Male	brain
40	chr6:33673400-33676600	Weak transcription	Fetal Lung	lung
41	chr6:33673800-33676600	Strong transcription	Fetal Thymus	thymus
42	chr6:33673800-33678000	Strong transcription	Fetal Stomach	stomach
43	chr6:33673800-33678400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr6:33674000-33676800	Strong transcription	Lung	lung
45	chr6:33674200-33678400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr6:33674400-33677600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:33674400-33677800	Strong transcription	Fetal Intestine Large	intestine
48	chr6:33674400-33678200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:33674400-33678200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:33674400-33678200	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links