Variant report

Variant	rs13214027
Chromosome Location	chr6:26573631-26573632
allele	C/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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26571513..26576040-chr6:26594296..26598668,8	MCF-7	breast:
2	chr6:26571842..26573812-chr6:27115017..27116978,2	K562	blood:
3	chr6:26532740..26539448-chr6:26569667..26573975,11	K562	blood:
4	chr6:26568887..26570876-chr6:26573166..26576074,2	MCF-7	breast:
5	chr6:26571551..26574960-chr6:26589936..26592999,3	MCF-7	breast:
6	chr6:26573140..26573693-chr6:26596604..26597267,2	Hela-S3	cervix:
7	chr6:26328751..26331113-chr6:26570899..26573999,3	K562	blood:
8	chr6:26571775..26574156-chr6:27139897..27141601,2	MCF-7	breast:
9	chr6:26569051..26574263-chr6:27058255..27061104,5	K562	blood:
10	chr6:26566413..26579648-chr6:26592370..26599609,38	K562	blood:
11	chr6:26572187..26574794-chr6:27094874..27097945,3	K562	blood:
12	chr6:26573047..26575181-chr6:27114968..27116628,2	MCF-7	breast:
13	chr6:26318750..26323113-chr6:26568559..26574896,7	K562	blood:
14	chr6:26291552..26293957-chr6:26573124..26576055,2	K562	blood:
15	chr6:26571063..26574475-chr6:27099949..27102316,3	K562	blood:
16	chr6:26197063..26201170-chr6:26570047..26573982,4	K562	blood:
17	chr6:26572487..26574347-chr6:26595749..26596943,8	MCF-7	breast:
18	chr6:26329307..26333799-chr6:26568024..26573999,9	K562	blood:
19	chr6:26382743..26384824-chr6:26572205..26574476,2	K562	blood:
20	chr6:26340224..26344158-chr6:26569567..26573981,6	K562	blood:
21	chr6:26174601..26176102-chr6:26570982..26573796,2	K562	blood:
22	chr6:26204076..26206640-chr6:26570365..26573810,4	K562	blood:
23	chr6:26572522..26574158-chr6:26595663..26596592,7	K562	blood:
24	chr6:26248134..26251436-chr6:26571961..26574933,3	K562	blood:
25	chr6:26572998..26574679-chr6:26574747..26576254,2	MCF-7	breast:
26	chr6:26340224..26342444-chr6:26572464..26573981,2	K562	blood:
27	chr6:26568033..26580216-chr6:26588796..26603066,49	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124508	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000220875	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10484443	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs11967935	0.83[ASN][1000 genomes]
rs12176129	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13210025	0.88[JPT][hapmap]
rs16891725	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16901784	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1977	0.84[CEU][hapmap]
rs1978	0.84[CEU][hapmap]
rs1979	0.91[CEU][hapmap]
rs2072803	0.85[CEU][hapmap]
rs2072806	0.85[CEU][hapmap]
rs2073529	0.84[CEU][hapmap]
rs2073531	0.85[CEU][hapmap]
rs2076030	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs2093169	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2295593	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2393667	0.85[CEU][hapmap]
rs28360517	0.80[AMR][1000 genomes]
rs3734544	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3757150	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3799383	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3999471	0.92[JPT][hapmap]
rs4634439	0.92[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs67234939	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6911765	0.88[CHB][hapmap]
rs6920256	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7740197	0.92[JPT][hapmap]
rs7759969	0.85[JPT][hapmap]
rs7773938	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9295702	0.93[JPT][hapmap]
rs9348716	0.85[CEU][hapmap]
rs9348718	0.88[CHB][hapmap]
rs9348726	0.80[AMR][1000 genomes]
rs9358937	0.85[CEU][hapmap]
rs9358938	0.83[CEU][hapmap]
rs9358944	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9358945	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9358946	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9366656	0.85[CEU][hapmap]
rs9366658	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9379875	0.85[CEU][hapmap]
rs9379880	0.80[ASN][1000 genomes]
rs9379882	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9379891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9379893	0.92[JPT][hapmap]
rs9379895	0.92[JPT][hapmap]
rs9379897	0.92[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs9379899	0.92[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs9379901	0.80[AMR][1000 genomes]
rs9379907	0.92[JPT][hapmap]
rs9393713	0.84[CEU][hapmap]
rs9393718	0.85[CEU][hapmap]
rs9393727	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393737	0.92[JPT][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13214027	BTN3A2	cis	Artery Tibial	GTEx
rs13214027	BTN3A2	cis	lung	GTEx
rs13214027	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs13214027	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs13214027	BTN3A2	cis	Thyroid	GTEx
rs13214027	BTN3A2	cis	Whole Blood	GTEx
rs13214027	BTN3A2	cis	normal skin	skin_eQTL
rs13214027	BTN3A2	cis	Muscle Skeletal	GTEx
rs13214027	BTN3A2	cis	Heart Left Ventricle	GTEx
rs13214027	BTN3A2	cis	lesional skin	skin_eQTL
rs13214027	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs13214027	BTN3A2	cis	Esophagus Muscularis	GTEx
rs13214027	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13214027	BTN3A2	cis	Esophagus Mucosa	GTEx
rs13214027	BTN3A2	cis	Nerve Tibial	GTEx
rs13214027	BTN3A2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26569600-26577600	Weak transcription	Spleen	Spleen
2	chr6:26573000-26576600	Weak transcription	NHLF	lung
3	chr6:26573000-26576800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:26573000-26576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:26573000-26577000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:26573000-26577200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:26573000-26577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:26573200-26574000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:26573200-26576000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:26573200-26576000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:26573200-26576600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:26573200-26576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:26573200-26577000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:26573200-26577000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:26573200-26577400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:26573400-26574600	Enhancers	HepG2	liver
17	chr6:26573400-26575800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:26573400-26575800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:26573400-26575800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:26573400-26575800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:26573400-26575800	Weak transcription	Hela-S3	cervix
22	chr6:26573400-26576000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:26573400-26576000	Weak transcription	A549	lung
24	chr6:26573400-26576200	Weak transcription	NHEK	skin
25	chr6:26573400-26576400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:26573400-26576400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:26573400-26576400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:26573400-26576600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:26573400-26576600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:26573400-26576800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:26573400-26576800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:26573400-26576800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:26573400-26576800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:26573400-26577000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:26573400-26577000	Weak transcription	HMEC	breast
36	chr6:26573400-26577200	Weak transcription	Dnd41	blood
37	chr6:26573400-26577400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:26573400-26577400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:26573400-26577400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:26573600-26574000	Enhancers	GM12878-XiMat	blood
41	chr6:26573600-26574000	Enhancers	K562	blood
42	chr6:26573600-26575600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:26573600-26575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:26573600-26575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:26573600-26575800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:26573600-26575800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:26573600-26576400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr6:26573600-26576800	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links