Variant report

Variant	rs12673800
Chromosome Location	chr7:6741407-6741408
allele	C/T
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	chr7:6741285-6741423	ProgFib	skin:	n/a	n/a
2	POLR2A	chr7:6741390-6741476	GM12878	blood:	n/a	n/a
3	STAT5A	chr7:6741348-6742217	GM12878	blood:	n/a	n/a
4	STAT5A	chr7:6740731-6742198	K562	blood:	n/a	n/a
5	POLR2A	chr7:6741256-6741432	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6727828..6730097-chr7:6741325..6744372,3	MCF-7	breast:

Variant related genes	Relation type
ZNF12	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10226798	0.87[ASN][1000 genomes]
rs10244591	0.92[JPT][hapmap]
rs10255119	0.83[EUR][1000 genomes]
rs10271259	0.85[EUR][1000 genomes]
rs10272921	0.92[JPT][hapmap]
rs10951991	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10951994	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs12537448	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13224907	0.92[JPT][hapmap]
rs13247186	0.90[JPT][hapmap]
rs1464922	0.91[EUR][1000 genomes]
rs1464923	0.94[EUR][1000 genomes]
rs2140909	0.82[CHB][hapmap]
rs2881352	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3735302	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3757481	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs3757483	0.82[EUR][1000 genomes]
rs3801033	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3801034	0.91[ASN][1000 genomes]
rs3801036	0.95[ASN][1000 genomes]
rs3801038	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801039	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs56257118	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58569329	0.85[EUR][1000 genomes]
rs58738503	0.83[EUR][1000 genomes]
rs60514449	0.82[EUR][1000 genomes]
rs62439670	0.85[EUR][1000 genomes]
rs62439674	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62439695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62439697	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62441324	0.83[EUR][1000 genomes]
rs6463576	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs6463580	0.92[JPT][hapmap]
rs6944332	0.94[CHD][hapmap];0.92[JPT][hapmap]
rs6948691	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6953825	0.92[JPT][hapmap]
rs6954172	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs6964079	1.00[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6965641	0.94[EUR][1000 genomes]
rs6969066	0.82[EUR][1000 genomes]
rs6971621	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6974325	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6979127	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7357087	0.81[ASN][1000 genomes]
rs7779296	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs7798471	0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7804259	1.00[JPT][hapmap]
rs7808550	0.88[EUR][1000 genomes]
rs9639027	0.92[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
4	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv3343175	chr7:6741252-6743800	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6712400-6744000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:6718600-6742600	ZNF genes & repeats	Liver	Liver
3	chr7:6721400-6745200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr7:6721600-6743800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr7:6721600-6744600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:6721600-6745400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:6721800-6744000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:6722400-6745000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr7:6722600-6745000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:6723600-6745000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:6723600-6745400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:6723800-6745000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:6724000-6744800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:6725000-6741800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:6725000-6744800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:6725800-6745000	ZNF genes & repeats	NH-A	brain
17	chr7:6726000-6741600	ZNF genes & repeats	Dnd41	blood
18	chr7:6726000-6742200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr7:6726000-6743600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr7:6726000-6744800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr7:6726000-6745000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:6726000-6745000	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr7:6726000-6745200	ZNF genes & repeats	A549	lung
24	chr7:6726200-6742200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr7:6726200-6742200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
26	chr7:6726200-6743600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:6726200-6743600	ZNF genes & repeats	NHEK	skin
28	chr7:6726200-6743800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:6726200-6743800	ZNF genes & repeats	HMEC	breast
30	chr7:6726200-6745000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
31	chr7:6726200-6745000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr7:6726200-6745000	ZNF genes & repeats	Fetal Lung	lung
33	chr7:6726400-6743600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr7:6726400-6744800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr7:6726600-6745000	ZNF genes & repeats	GM12878-XiMat	blood
36	chr7:6726800-6742200	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr7:6730200-6741600	Strong transcription	HepG2	liver
38	chr7:6730200-6742000	ZNF genes & repeats	Ovary	ovary
39	chr7:6730400-6744000	ZNF genes & repeats	Colonic Mucosa	Colon
40	chr7:6730800-6745000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:6731200-6745400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:6732600-6744000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr7:6733200-6745200	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr7:6733600-6744800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:6735600-6741800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:6736200-6743600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:6737000-6742800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:6737000-6744000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:6737600-6741800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr7:6737600-6742600	Strong transcription	Stomach Smooth Muscle	stomach

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