Variant report

Variant	rs12047464
Chromosome Location	chr1:169850410-169850411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169847146..169850317-chr1:169850331..169854277,4	K562	blood:
2	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
3	chr1:169845321..169846924-chr1:169848823..169850416,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10489171	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919229	0.87[CHB][hapmap]
rs10919246	0.82[CHB][hapmap]
rs12024321	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025244	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs12025442	0.81[ASN][1000 genomes]
rs12025581	0.81[ASN][1000 genomes]
rs12028435	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029611	0.81[ASN][1000 genomes]
rs12031046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12038307	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042277	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043338	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs12046689	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12239757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16828193	0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16862714	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862755	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2179172	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs2272913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272914	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28477509	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35296671	0.89[ASN][1000 genomes]
rs35372000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766133	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766136	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766149	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766153	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57868479	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58583023	0.81[ASN][1000 genomes]
rs58910844	0.81[ASN][1000 genomes]
rs72637238	0.81[ASN][1000 genomes]
rs72637239	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72637240	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72637241	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72637242	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72637243	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72637244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730083	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9287096	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9659149	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
3	chr1:169833800-169860200	Weak transcription	HMEC	breast
4	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
5	chr1:169842400-169850800	Weak transcription	Esophagus	oesophagus
6	chr1:169842400-169851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:169842400-169851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:169843000-169851000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:169843600-169855000	Weak transcription	NHEK	skin
13	chr1:169843800-169850800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:169844000-169851200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:169844000-169851200	Weak transcription	Pancreas	Pancrea
16	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:169844400-169857400	Weak transcription	K562	blood
18	chr1:169844800-169851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:169844800-169854600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:169844800-169855400	Weak transcription	Hela-S3	cervix
21	chr1:169844800-169856000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:169845000-169854000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:169845200-169850800	Weak transcription	Brain Germinal Matrix	brain
25	chr1:169845200-169850800	Weak transcription	Lung	lung
26	chr1:169845200-169851000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:169845200-169851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:169845200-169853800	Weak transcription	Fetal Kidney	kidney
29	chr1:169845200-169854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:169845200-169855000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:169845200-169857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:169845200-169857200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:169845200-169857400	Weak transcription	HUVEC	blood vessel
34	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
35	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:169845400-169853400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
39	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:169845600-169850600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:169845600-169855000	Weak transcription	Fetal Brain Female	brain
42	chr1:169845800-169855600	Weak transcription	A549	lung
43	chr1:169846000-169854600	Weak transcription	HSMMtube	muscle
44	chr1:169846000-169858000	Weak transcription	Small Intestine	intestine
45	chr1:169846600-169851000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:169846600-169851000	Weak transcription	Fetal Intestine Small	intestine
47	chr1:169846600-169851000	Weak transcription	Fetal Stomach	stomach
48	chr1:169846800-169850600	Weak transcription	Gastric	stomach
49	chr1:169847000-169850600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:169847000-169850800	Weak transcription	Aorta	Aorta

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