Variant report

Variant	rs17080102
Chromosome Location	chr6:151004770-151004771
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	chr6:151004338..151007034-chr6:151012043..151014103,2	MCF-7	breast:
2	chr6:150997606..151001974-chr6:151004328..151007109,4	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12661140	1.00[CEU][hapmap];0.91[AMR][1000 genomes]
rs12663498	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12664595	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1494308	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1552886	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1552889	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17080057	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17080062	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17080069	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17080087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17080089	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17080091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17080093	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57139556	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59155780	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62434109	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62434110	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62434111	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62434119	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62434120	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62434122	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62434123	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62434124	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62434125	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62434129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654698	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6557083	1.00[JPT][hapmap]
rs6929935	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9322273	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9322274	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9322275	0.81[AMR][1000 genomes]
rs9322277	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9322278	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9397343	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood pressure	23972371	GWAS catalog

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150980600-151008800	Weak transcription	Gastric	stomach
2	chr6:150980800-151014800	Weak transcription	Pancreas	Pancrea
3	chr6:150989400-151007800	Weak transcription	Ovary	ovary
4	chr6:150990600-151008800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:150990600-151016600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:150990800-151011800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:150995000-151008800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:150995400-151005400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:150995400-151008800	Weak transcription	Small Intestine	intestine
10	chr6:150995600-151006000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:150995600-151006200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:150996600-151008000	Weak transcription	Fetal Intestine Large	intestine
13	chr6:150998200-151006000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:151000800-151010000	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:151001000-151006600	Enhancers	Spleen	Spleen
16	chr6:151001600-151008200	Genic enhancers	Fetal Thymus	thymus
17	chr6:151002200-151005000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:151002400-151007800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:151002800-151004800	Enhancers	Fetal Muscle Trunk	muscle
20	chr6:151003000-151004800	Enhancers	Esophagus	oesophagus
21	chr6:151003000-151006200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:151003000-151006400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:151003000-151006800	Strong transcription	Fetal Stomach	stomach
24	chr6:151003200-151004800	Enhancers	HUVEC	blood vessel
25	chr6:151003200-151006600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:151003400-151007400	Genic enhancers	Thymus	Thymus
27	chr6:151003600-151006200	Enhancers	Primary T cells from cord blood	blood
28	chr6:151003600-151006600	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:151003600-151007600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:151003600-151011400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:151003800-151005000	Enhancers	Right Atrium	heart
32	chr6:151003800-151007400	Weak transcription	NHEK	skin
33	chr6:151003800-151015000	Weak transcription	Brain Substantia Nigra	brain
34	chr6:151004000-151004800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:151004000-151004800	Weak transcription	Brain Anterior Caudate	brain
36	chr6:151004000-151004800	Weak transcription	Placenta	Placenta
37	chr6:151004000-151004800	Weak transcription	Right Ventricle	heart
38	chr6:151004000-151005200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:151004000-151007000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:151004000-151007000	Weak transcription	HMEC	breast
41	chr6:151004200-151004800	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:151004200-151004800	Enhancers	GM12878-XiMat	blood
43	chr6:151004200-151005400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr6:151004200-151006000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:151004200-151006600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr6:151004200-151007000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:151004200-151007000	Weak transcription	Fetal Kidney	kidney
48	chr6:151004400-151004800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr6:151004600-151005000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:151004600-151005400	Flanking Active TSS	Lung	lung

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