Variant report

Variant	rs11964178
Chromosome Location	chr6:109562035-109562036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109559579..109562142-chr6:109563967..109566714,2	MCF-7	breast:
2	chr6:109561439..109564870-chr6:109795296..109799146,3	K562	blood:
3	chr6:109550909..109553791-chr6:109560961..109563998,3	K562	blood:
4	chr6:109561446..109564141-chr6:109698737..109700867,2	K562	blood:
5	chr6:109561591..109563297-chr6:109615936..109618604,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11153161	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1271693	0.85[ASN][1000 genomes]
rs13196590	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13211313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13211944	0.90[ASN][1000 genomes]
rs1741923	0.93[ASN][1000 genomes]
rs34774766	0.93[ASN][1000 genomes]
rs351716	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351717	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351718	0.95[ASN][1000 genomes]
rs351719	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351722	0.95[ASN][1000 genomes]
rs351723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351724	0.81[EUR][1000 genomes]
rs351725	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs351726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs351728	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs351731	0.90[ASN][1000 genomes]
rs351732	0.90[ASN][1000 genomes]
rs351735	0.91[ASN][1000 genomes]
rs351736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs351737	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs351742	0.82[TSI][hapmap]
rs351744	0.96[ASN][1000 genomes]
rs351746	0.93[ASN][1000 genomes]
rs351747	0.93[ASN][1000 genomes]
rs351750	0.93[ASN][1000 genomes]
rs351751	0.94[ASN][1000 genomes]
rs353052	0.91[ASN][1000 genomes]
rs371960	0.82[TSI][hapmap]
rs377436	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs388526	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs396635	0.93[ASN][1000 genomes]
rs399561	0.82[TSI][hapmap]
rs408944	0.92[ASN][1000 genomes]
rs410449	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs412754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs418093	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs421790	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs422113	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs427960	0.82[TSI][hapmap]
rs429534	0.93[ASN][1000 genomes]
rs436880	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs446974	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs448496	0.94[ASN][1000 genomes]
rs449736	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs449850	0.82[TSI][hapmap]
rs566164	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs59673	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6919423	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925339	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs830552	0.94[ASN][1000 genomes]
rs830554	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs830556	0.94[ASN][1000 genomes]
rs9320278	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9384701	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9386774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9791268	0.81[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527657	chr6:109533385-109579675	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11964178	GSTM2P1	cis	parietal	SCAN
rs11964178	ATG5	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109556800-109562800	Enhancers	Primary hematopoietic stem cells	blood
2	chr6:109556800-109564200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:109557200-109565000	Enhancers	NHDF-Ad	bronchial
4	chr6:109557400-109562200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:109557600-109565200	Enhancers	Hela-S3	cervix
6	chr6:109558200-109565000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:109558200-109565200	Enhancers	Osteobl	bone
8	chr6:109558200-109572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:109558600-109562800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:109558800-109566400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:109559000-109563400	Enhancers	Primary B cells from cord blood	blood
12	chr6:109559000-109564000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:109559000-109564200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:109559200-109564200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:109559400-109563600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:109559400-109563600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:109559600-109562600	Enhancers	Adipose Nuclei	Adipose
18	chr6:109560000-109562200	Enhancers	Brain Angular Gyrus	brain
19	chr6:109560000-109562200	Enhancers	Brain Substantia Nigra	brain
20	chr6:109560000-109562600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:109560000-109563000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:109560400-109562200	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:109560400-109562600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:109560400-109563600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr6:109560400-109564200	Enhancers	HSMM	muscle
26	chr6:109561200-109562400	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr6:109561400-109562200	Enhancers	Fetal Muscle Leg	muscle
28	chr6:109561600-109566200	Enhancers	K562	blood
29	chr6:109561800-109562600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr6:109561800-109562800	Enhancers	HSMMtube	muscle
31	chr6:109562000-109562800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:109562000-109563200	Weak transcription	Left Ventricle	heart
33	chr6:109562000-109563400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:109562000-109563400	Weak transcription	Psoas Muscle	Psoas
35	chr6:109562000-109563600	Enhancers	HepG2	liver
36	chr6:109562000-109564000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:109562000-109572400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links