Variant report

Variant	rs9461459
Chromosome Location	chr6:28361916-28361917
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28186853..28189269-chr6:28360764..28363379,2	K562	blood:
2	chr6:28332159..28333981-chr6:28361643..28364361,2	K562	blood:
3	chr6:28361480..28362110-chr6:28653554..28654437,2	K562	blood:
4	chr6:28359897..28362506-chr6:28613582..28616883,3	K562	blood:
5	chr6:28361885..28364070-chr6:28448691..28451219,2	K562	blood:
6	chr6:28303466..28305009-chr6:28358955..28361935,2	K562	blood:
7	chr6:28361357..28362258-chr6:28510286..28511051,2	MCF-7	breast:
8	chr6:28321911..28323574-chr6:28361622..28363412,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000235570	Chromatin interaction
ENSG00000272278	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1005127	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054372	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124131	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751693	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752496	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11752919	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11754208	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755942	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760133	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12697938	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201726	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13201753	0.94[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs13207208	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13210866	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13215476	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1339898	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13437294	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361385	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416918	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558205	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1591913	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894021	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16894060	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894095	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16894108	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2027361	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041230	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071965	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213228	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2531804	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs28360638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34513104	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34924864	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35191424	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35560946	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35599905	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36018474	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734563	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800328	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4254981	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4357130	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580862	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4642462	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66542396	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67211468	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899389	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899603	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903535	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6907950	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6908137	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6917130	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6922169	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922374	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6922429	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6927229	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6928773	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929825	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6939966	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs740621	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740622	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7451726	0.84[ASN][1000 genomes]
rs7740351	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7749736	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754960	0.80[YRI][hapmap]
rs7759191	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764722	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764737	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773051	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461455	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461456	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461458	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468354	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468355	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468357	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468360	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468367	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468368	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468370	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9461459	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9461459	RP5-874C20.3	cis	Thyroid	GTEx
rs9461459	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs9461459	AL022393.7	cis	Heart Left Ventricle	GTEx
rs9461459	ZSCAN31	cis	Thyroid	GTEx
rs9461459	ZSCAN31	cis	lung	GTEx
rs9461459	AL022393.7	cis	Muscle Skeletal	GTEx
rs9461459	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9461459	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs9461459	ZSCAN31	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28351600-28364600	Weak transcription	Right Atrium	heart
2	chr6:28352000-28362000	Strong transcription	Primary T cells from cord blood	blood
3	chr6:28352200-28365800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:28352600-28362000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:28352600-28362600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:28352600-28364200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:28352600-28364400	Strong transcription	Fetal Thymus	thymus
8	chr6:28352600-28364600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:28352600-28365400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:28352600-28365800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:28353000-28362200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:28353000-28364800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:28353200-28362000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:28354000-28364600	Strong transcription	Fetal Muscle Leg	muscle
15	chr6:28354200-28365600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr6:28354400-28364800	Strong transcription	Fetal Stomach	stomach
17	chr6:28354800-28363800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr6:28355600-28362000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:28355800-28364800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:28356000-28362000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:28356200-28362000	Strong transcription	Osteobl	bone
22	chr6:28356400-28362600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:28356600-28363000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:28358200-28362000	ZNF genes & repeats	GM12878-XiMat	blood
25	chr6:28358600-28364200	Weak transcription	Stomach Mucosa	stomach
26	chr6:28358600-28365000	Weak transcription	Fetal Heart	heart
27	chr6:28358800-28362000	Strong transcription	K562	blood
28	chr6:28359000-28364600	Weak transcription	NHEK	skin
29	chr6:28359200-28365000	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:28359200-28366000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:28359200-28366200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:28359200-28366600	Weak transcription	Right Ventricle	heart
33	chr6:28359400-28362200	Weak transcription	Primary B cells from cord blood	blood
34	chr6:28359400-28363800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:28359400-28364400	Weak transcription	Pancreas	Pancrea
36	chr6:28359400-28364400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:28359400-28364400	Weak transcription	NHDF-Ad	bronchial
38	chr6:28359400-28364600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:28359400-28364800	Weak transcription	Esophagus	oesophagus
40	chr6:28359400-28365800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:28359400-28365800	Weak transcription	Gastric	stomach
42	chr6:28359400-28365800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:28359400-28365800	Weak transcription	Small Intestine	intestine
44	chr6:28359400-28366000	Weak transcription	HSMMtube	muscle
45	chr6:28359400-28366600	Weak transcription	Psoas Muscle	Psoas
46	chr6:28359400-28366800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:28359600-28362000	Weak transcription	Hela-S3	cervix
48	chr6:28359600-28363200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:28359600-28366800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:28359800-28366800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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