Variant report

Variant	rs6679646
Chromosome Location	chr1:169789149-169789150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169763673..169765585-chr1:169787149..169789701,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10159425	0.81[EUR][1000 genomes]
rs10489170	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489177	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800477	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10800482	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10919260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10919270	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs10919271	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap]
rs10919272	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs11804170	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs12049325	0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12128754	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12135826	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12138675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12401338	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12757747	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12760433	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2143121	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2272916	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35275808	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35414012	0.80[AMR][1000 genomes]
rs35688996	0.88[JPT][hapmap]
rs6427223	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6427229	0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs6658548	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6670253	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6688806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74122428	0.82[AMR][1000 genomes]
rs7533194	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7552710	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs882595	1.00[CEU][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9787237	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169793200	Weak transcription	Aorta	Aorta
2	chr1:169764800-169793200	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:169764800-169793400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:169764800-169795200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:169764800-169796200	Weak transcription	Spleen	Spleen
6	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
7	chr1:169764800-169818200	Weak transcription	Lung	lung
8	chr1:169764800-169823600	Weak transcription	Gastric	stomach
9	chr1:169765000-169793200	Weak transcription	Fetal Brain Male	brain
10	chr1:169765000-169808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:169765200-169793200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:169765200-169793200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:169765200-169793400	Weak transcription	Fetal Kidney	kidney
15	chr1:169765200-169797400	Weak transcription	HSMMtube	muscle
16	chr1:169765200-169802000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:169765200-169807800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:169765200-169808000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:169765200-169809000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:169765200-169814800	Weak transcription	Brain Anterior Caudate	brain
21	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
23	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
24	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
25	chr1:169765400-169796800	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:169765400-169798400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:169765400-169798400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:169765400-169808000	Weak transcription	Fetal Heart	heart
29	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
30	chr1:169765600-169808000	Weak transcription	Small Intestine	intestine
31	chr1:169765600-169818200	Weak transcription	NHLF	lung
32	chr1:169765800-169793200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:169765800-169808000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:169766000-169796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:169766000-169797000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:169766000-169797400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:169773400-169796200	Weak transcription	HMEC	breast
40	chr1:169773400-169798400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:169773400-169808000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:169773800-169796200	Weak transcription	NH-A	brain
43	chr1:169773800-169796200	Weak transcription	Osteobl	bone
44	chr1:169774600-169791000	Weak transcription	Placenta	Placenta
45	chr1:169774600-169793200	Weak transcription	HepG2	liver
46	chr1:169774800-169791200	Weak transcription	Fetal Stomach	stomach
47	chr1:169774800-169793200	Weak transcription	Left Ventricle	heart
48	chr1:169774800-169793200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:169774800-169796200	Weak transcription	HUVEC	blood vessel
50	chr1:169774800-169796400	Weak transcription	Fetal Intestine Large	intestine

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