Variant report

Variant	rs3132682
Chromosome Location	chr6:30044388-30044389
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
2	chr6:30041669..30045289-chr6:30052962..30056751,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs166327	0.80[ASN][1000 genomes]
rs2057728	0.96[EUR][1000 genomes]
rs2240619	0.83[ASN][1000 genomes]
rs2394736	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3094144	0.85[ASN][1000 genomes]
rs3098018	0.81[ASN][1000 genomes]
rs3115635	0.82[ASN][1000 genomes]
rs3121594	0.85[ASN][1000 genomes]
rs3869065	0.85[ASN][1000 genomes]
rs3869070	0.86[ASN][1000 genomes]
rs6457126	0.85[ASN][1000 genomes]
rs6457144	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6904455	0.95[EUR][1000 genomes]
rs6909253	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6909437	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6923777	0.81[ASN][1000 genomes]
rs7382061	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261244	0.85[ASN][1000 genomes]
rs9261301	0.91[ASN][1000 genomes]
rs9261394	0.96[EUR][1000 genomes]
rs9261395	0.94[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3132682	HLA-A	cis	lymphoblastoid	GTEx
rs3132682	BTN2A1	cis	cerebellum	SCAN
rs3132682	KIT	trans	multi-tissue	Pritchard
rs3132682	HLA-A	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30042200-30044400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:30042800-30044400	Bivalent Enhancer	Fetal Thymus	thymus
3	chr6:30043000-30045800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:30043200-30044600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:30043200-30045800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:30043200-30045800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:30043400-30044400	Flanking Active TSS	NHEK	skin
8	chr6:30043400-30045000	Enhancers	Dnd41	blood
9	chr6:30043600-30044400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:30043600-30044600	Enhancers	Primary T cells from cord blood	blood
11	chr6:30043600-30044600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
12	chr6:30043600-30044600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr6:30043600-30045400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:30043600-30045600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:30043600-30045600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:30043800-30044400	Bivalent Enhancer	Fetal Intestine Small	intestine
17	chr6:30043800-30044600	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr6:30043800-30044800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:30043800-30044800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:30043800-30045800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:30044000-30044400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
22	chr6:30044000-30044400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr6:30044000-30044400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr6:30044000-30044400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
25	chr6:30044000-30044600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
26	chr6:30044000-30044800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:30044200-30044400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr6:30044200-30044600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:30044200-30044600	Enhancers	Hela-S3	cervix
30	chr6:30044200-30044800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:30044200-30044800	Enhancers	HMEC	breast
32	chr6:30044200-30045800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:30044200-30045800	Bivalent Enhancer	HepG2	liver

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