Variant report

Variant	rs11579934
Chromosome Location	chr1:62732945-62732946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:62732926-62733043	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
KANK4	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10889316	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11207950	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207951	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207952	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11583803	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584786	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs12127930	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs1325738	0.85[CHB][hapmap]
rs1555832	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1886830	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1925825	0.85[CHB][hapmap]
rs2666467	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2765254	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2765255	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2765260	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2765262	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs3850629	0.81[EUR][1000 genomes]
rs3861936	0.81[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4609464	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915810	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6664843	0.87[ASN][1000 genomes]
rs6680736	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6691591	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6695520	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3408127	chr1:62729964-62734262	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:62728000-62734800	Weak transcription	Fetal Brain Male	brain
4	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
5	chr1:62729400-62734400	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr1:62729600-62734000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:62729600-62736800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:62729600-62737400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:62729600-62737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:62729600-62737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:62729800-62737400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:62730800-62734000	Strong transcription	Adipose Nuclei	Adipose
14	chr1:62731400-62734600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:62731400-62734800	Strong transcription	HepG2	liver
16	chr1:62731800-62733200	Genic enhancers	Pancreas	Pancrea
17	chr1:62732000-62734000	Genic enhancers	Fetal Stomach	stomach
18	chr1:62732000-62734800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:62732000-62734800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:62732200-62733000	Enhancers	Brain Germinal Matrix	brain
21	chr1:62732200-62737000	Weak transcription	Esophagus	oesophagus
22	chr1:62732200-62737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:62732400-62733800	Weak transcription	Gastric	stomach
24	chr1:62732400-62734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:62732400-62737000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:62732400-62737400	Weak transcription	Fetal Kidney	kidney
27	chr1:62732400-62737600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:62732400-62737600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:62732400-62737600	Weak transcription	Placenta	Placenta
30	chr1:62732400-62740000	Weak transcription	Liver	Liver
31	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:62732600-62733200	Enhancers	Fetal Lung	lung
33	chr1:62732800-62734000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:62732800-62737600	Weak transcription	Fetal Intestine Small	intestine

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