Variant report

Variant	rs1150711
Chromosome Location	chr6:28208535-28208536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28207533..28210874-chr6:28216267..28219988,4	MCF-7	breast:
2	chr6:28206024..28209591-chr6:28211608..28215918,4	MCF-7	breast:
3	chr6:28103041..28105125-chr6:28207182..28210189,3	K562	blood:
4	chr6:28202226..28208942-chr6:28209296..28217649,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261839	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1052215	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs1150668	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1150691	0.83[CHB][hapmap]
rs1150694	0.90[JPT][hapmap]
rs1150705	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1150707	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1150709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1150716	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1150718	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1150721	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs1150724	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs1150726	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs12214383	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs1225618	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs1225710	0.86[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs1225715	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs1233660	0.83[ASN][1000 genomes]
rs1233713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13408	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs1416920	0.81[TSI][hapmap]
rs149956	0.81[JPT][hapmap]
rs1531681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs1558205	0.83[CEU][hapmap]
rs1654774	0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs1736891	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1736895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs1736904	0.83[CHB][hapmap]
rs1778484	0.83[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs1997660	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2021826	0.90[JPT][hapmap]
rs203869	0.86[JPT][hapmap]
rs203878	0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs213238	0.86[JPT][hapmap]
rs213240	0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs2142730	0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2394049	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2622320	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2622322	0.90[JPT][hapmap]
rs2791333	0.83[CHD][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2859348	0.86[CHB][hapmap]
rs4713158	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs707907	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7206	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs853683	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs853684	0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs853690	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs853693	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9301	0.91[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs9468333	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468344	0.81[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs1150711	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1150711	ZKSCAN3	cis	cerebellum	SCAN
rs1150711	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1150711	ZSCAN31	cis	lung	GTEx
rs1150711	NKAPL	cis	parietal	SCAN
rs1150711	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs1150711	AL022393.7	cis	Thyroid	GTEx
rs1150711	AL022393.7	cis	Nerve Tibial	GTEx
rs1150711	HIST1H1D	cis	parietal	SCAN
rs1150711	HIST1H2BO	cis	parietal	SCAN
rs1150711	ZSCAN23	cis	parietal	SCAN
rs1150711	ZNF192	cis	cerebellum	SCAN
rs1150711	ZSCAN31	cis	Stomach	GTEx
rs1150711	ZNF323	cis	parietal	SCAN
rs1150711	ZSCAN23	cis	cerebellum	SCAN
rs1150711	RP5-874C20.3	cis	Thyroid	GTEx
rs1150711	AL022393.7	cis	Artery Tibial	GTEx
rs1150711	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1150711	ZSCAN31	cis	Thyroid	GTEx
rs1150711	ZKSCAN3	cis	parietal	SCAN
rs1150711	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs1150711	ZNF187	cis	cerebellum	SCAN
rs1150711	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1150711	AL022393.7	cis	Muscle Skeletal	GTEx
rs1150711	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1150711	ZNF323	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193600-28213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:28193800-28211800	Weak transcription	Fetal Thymus	thymus
3	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
5	chr6:28194000-28211000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:28194000-28211800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:28194000-28212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:28194000-28213000	Weak transcription	Thymus	Thymus
9	chr6:28194000-28213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:28196800-28212400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:28196800-28212400	Weak transcription	Small Intestine	intestine
12	chr6:28196800-28213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:28197000-28212400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:28198800-28212200	Weak transcription	Hela-S3	cervix
15	chr6:28199200-28213200	Weak transcription	Colonic Mucosa	Colon
16	chr6:28199800-28213600	Weak transcription	NHDF-Ad	bronchial
17	chr6:28200400-28212400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:28200400-28212600	Weak transcription	NHEK	skin
19	chr6:28200800-28212400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:28200800-28212600	Weak transcription	Fetal Heart	heart
21	chr6:28201000-28211000	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28201000-28211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:28201000-28212200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:28201000-28212200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:28201000-28212400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:28201000-28212400	Weak transcription	HMEC	breast
27	chr6:28201000-28212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28201000-28212800	Weak transcription	Pancreas	Pancrea
29	chr6:28201000-28212800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:28201000-28212800	Weak transcription	Right Ventricle	heart
31	chr6:28201200-28212200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:28201600-28211600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:28201600-28211800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:28201600-28212000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:28201600-28212400	Weak transcription	Esophagus	oesophagus
36	chr6:28201600-28212600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:28201600-28212600	Weak transcription	Brain Angular Gyrus	brain
38	chr6:28201600-28212600	Weak transcription	Fetal Brain Male	brain
39	chr6:28201600-28212800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:28201600-28212800	Weak transcription	Gastric	stomach
41	chr6:28201600-28213000	Weak transcription	HepG2	liver
42	chr6:28201600-28213400	Weak transcription	Fetal Kidney	kidney
43	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:28201800-28211000	Weak transcription	Psoas Muscle	Psoas
45	chr6:28201800-28211800	Weak transcription	Osteobl	bone
46	chr6:28201800-28212000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:28202000-28211400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:28202000-28211600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:28202000-28211800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:28202000-28212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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