Variant report

Variant	rs9261301
Chromosome Location	chr6:30041559-30041560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
2	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
3	chr6:30041144..30044066-chr6:30293669..30296230,2	MCF-7	breast:
4	chr6:30040732..30043488-chr6:30062276..30064354,2	K562	blood:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs166327	0.88[ASN][1000 genomes]
rs2240619	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394255	0.82[ASN][1000 genomes]
rs3094144	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3098018	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3115635	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3121594	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3132682	0.91[ASN][1000 genomes]
rs3869065	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3869070	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3873293	0.82[ASN][1000 genomes]
rs3891158	0.82[ASN][1000 genomes]
rs6457120	0.80[ASN][1000 genomes]
rs6457121	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457126	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6923777	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261006	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261244	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv884049	chr6:30037353-30047403	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9261301	HLA-A	cis	lymphoblastoid	seeQTL
rs9261301	GRM4	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30036800-30042400	Weak transcription	Hela-S3	cervix
2	chr6:30038000-30041800	Weak transcription	Ovary	ovary
3	chr6:30038400-30044000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:30038600-30042000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:30038800-30043400	Weak transcription	Dnd41	blood
6	chr6:30039000-30042000	Weak transcription	Lung	lung
7	chr6:30039600-30042200	Weak transcription	Right Atrium	heart
8	chr6:30039800-30041800	Weak transcription	Gastric	stomach
9	chr6:30040600-30041800	Weak transcription	HMEC	breast
10	chr6:30040800-30041600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:30041000-30041800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr6:30041200-30041600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
13	chr6:30041200-30041800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:30041200-30041800	Bivalent Enhancer	Placenta	Placenta
15	chr6:30041200-30042000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
16	chr6:30041200-30042200	Enhancers	Pancreas	Pancrea
17	chr6:30041200-30043600	Active TSS	Esophagus	oesophagus
18	chr6:30041400-30041600	Enhancers	NHEK	skin
19	chr6:30041400-30041800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr6:30041400-30041800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
21	chr6:30041400-30041800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:30041400-30041800	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr6:30041400-30042000	Bivalent Enhancer	Brain Germinal Matrix	brain
24	chr6:30041400-30042200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
25	chr6:30041400-30043000	Flanking Bivalent TSS/Enh	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links