Variant report

Variant	rs17505698
Chromosome Location	chr6:166929190-166929191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166928469..166930058-chr6:167040238..167042581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071242	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11961547	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962002	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962046	0.96[ASN][1000 genomes]
rs11962068	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962104	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11962129	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11962190	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962191	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962250	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11962691	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962718	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11964246	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11964912	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11967122	0.96[ASN][1000 genomes]
rs11968040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11969346	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11969535	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11969688	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11970138	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11970162	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11970189	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11970312	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12526968	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17584003	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33973677	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35007078	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778423	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799649	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799651	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799653	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799663	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57672678	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6903487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6908724	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6908895	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6923077	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6923273	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6924732	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs73788006	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73788028	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs743980	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754491	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	esv1806956	chr6:166928580-166938431	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166899400-166929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:166909600-166943800	Weak transcription	Colonic Mucosa	Colon
6	chr6:166912200-166931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:166913000-166952000	Weak transcription	Primary T cells from cord blood	blood
8	chr6:166916200-166954200	Weak transcription	Right Atrium	heart
9	chr6:166916400-166940400	Weak transcription	Fetal Heart	heart
10	chr6:166917200-166932000	Weak transcription	Primary B cells from cord blood	blood
11	chr6:166918400-166931400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:166921200-166930000	Weak transcription	Fetal Intestine Large	intestine
13	chr6:166921400-166930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:166921400-166930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:166921400-166943600	Weak transcription	Fetal Lung	lung
16	chr6:166921600-166932000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:166921600-166932000	Weak transcription	Fetal Kidney	kidney
18	chr6:166921600-166937400	Weak transcription	Fetal Brain Male	brain
19	chr6:166922400-166929400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:166923000-166930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:166923000-166930000	Weak transcription	Esophagus	oesophagus
22	chr6:166923000-166931400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:166923000-166937200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:166923000-166940400	Weak transcription	Aorta	Aorta
25	chr6:166923000-166943800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:166923200-166931200	Weak transcription	Brain Germinal Matrix	brain
27	chr6:166923200-166932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:166923200-166940200	Weak transcription	Ovary	ovary
29	chr6:166923200-166943200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:166923200-166943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:166923600-166936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:166923800-166930000	Weak transcription	Placenta	Placenta
33	chr6:166923800-166944400	Weak transcription	Psoas Muscle	Psoas
34	chr6:166923800-166953000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:166925000-166940400	Weak transcription	Adipose Nuclei	Adipose
36	chr6:166926200-166930400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:166926200-166930400	Strong transcription	Fetal Stomach	stomach
38	chr6:166926400-166929200	Strong transcription	Fetal Muscle Leg	muscle
39	chr6:166927000-166930400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:166927200-166938000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:166927600-166929400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:166927600-166929600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:166927600-166929600	Enhancers	HMEC	breast
44	chr6:166927600-166930400	Genic enhancers	Lung	lung
45	chr6:166927800-166930400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:166928000-166930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:166928000-166930400	Enhancers	Brain Angular Gyrus	brain
48	chr6:166928000-166930400	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:166928200-166930000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:166928200-166930400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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