Variant report

Variant	rs2394159
Chromosome Location	chr6:29702679-29702680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29702012..29703555-chr6:29719487..29721197,2	K562	blood:
2	chr6:29702235..29703896-chr6:29705917..29708900,2	K562	blood:

Variant related genes	Relation type
ENSG00000214922	Chromatin interaction
ENSG00000272236	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1362125	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362126	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1610741	0.86[ASN][1000 genomes]
rs1736905	0.81[ASN][1000 genomes]
rs2076176	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107184	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2394160	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394162	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2517939	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523387	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523388	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523389	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523393	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523395	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523396	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523397	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523402	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523404	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523405	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2735051	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735052	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735057	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735059	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2735060	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743917	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743918	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2743919	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743922	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2743949	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2743951	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844830	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844831	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844832	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844846	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3998799	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4988549	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7754067	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv883531	chr6:29692562-29705402	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	esv3386435	chr6:29702223-29704171	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2394159	HLA.A29.1	cis	multi-tissue	Pritchard
rs2394159	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2394159	HIST1H2BM	cis	cerebellum	SCAN
rs2394159	HLA-H	cis	lymphoblastoid	seeQTL
rs2394159	HLA-A	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
5	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
6	chr6:29693600-29715600	Weak transcription	NHLF	lung
7	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
10	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:29694000-29711400	Weak transcription	Gastric	stomach
13	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
14	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:29694200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:29696000-29705600	Weak transcription	Right Ventricle	heart
17	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:29696000-29715600	Weak transcription	Ovary	ovary
19	chr6:29696200-29703800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:29696200-29703800	Weak transcription	Left Ventricle	heart
21	chr6:29696200-29705600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:29696200-29705800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:29696200-29711800	Weak transcription	Adipose Nuclei	Adipose
24	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:29696200-29715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:29696200-29715600	Weak transcription	Liver	Liver
27	chr6:29696400-29710800	Weak transcription	Lung	lung
28	chr6:29696400-29711400	Weak transcription	Spleen	Spleen
29	chr6:29696400-29711800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:29696400-29712000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:29696400-29715400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:29696600-29715600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:29696800-29714600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:29696800-29715800	Weak transcription	Colonic Mucosa	Colon
35	chr6:29699200-29712400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:29700000-29715200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:29700600-29711600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:29701800-29702800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr6:29701800-29702800	Enhancers	HMEC	breast
40	chr6:29702000-29702800	Enhancers	GM12878-XiMat	blood
41	chr6:29702000-29711200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:29702000-29711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:29702200-29702800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:29702200-29702800	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:29702200-29702800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:29702200-29705400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:29702400-29702800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr6:29702400-29702800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:29702400-29702800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:29702400-29702800	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links