Variant report

Variant	rs17034639
Chromosome Location	chr12:104217799-104217800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104211016..104214804-chr12:104214822..104218776,4	K562	blood:
2	chr12:104213266..104215424-chr12:104217652..104220137,3	MCF-7	breast:
3	chr12:104214519..104222192-chr12:104231005..104236989,8	K562	blood:
4	chr12:104208479..104212455-chr12:104217163..104218930,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257754	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1057892	0.92[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs11111802	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs12422418	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12422615	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12422701	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12423476	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12423889	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423912	0.87[EUR][1000 genomes]
rs12423994	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12424929	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12424984	0.90[EUR][1000 genomes]
rs12425283	0.87[EUR][1000 genomes]
rs12425537	1.00[AFR][1000 genomes]
rs1437505	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1550207	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550208	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034593	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17034620	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034637	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034640	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17034642	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034645	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034648	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034650	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034662	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17034880	1.00[MKK][hapmap]
rs17180749	1.00[MKK][hapmap]
rs17794246	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1882019	1.00[MKK][hapmap]
rs2289258	0.83[EUR][1000 genomes]
rs2293626	1.00[MKK][hapmap]
rs3751196	0.84[CEU][hapmap];1.00[TSI][hapmap]
rs3751207	1.00[MKK][hapmap]
rs3751208	1.00[MKK][hapmap]
rs3812802	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3829300	1.00[MKK][hapmap]
rs4135082	1.00[MKK][hapmap]
rs4135085	1.00[MKK][hapmap]
rs4135087	1.00[MKK][hapmap]
rs55724382	0.84[EUR][1000 genomes]
rs55736751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55810720	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs55932227	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55949441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987022	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55993375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56123042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56143748	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56147174	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56255894	0.90[EUR][1000 genomes]
rs56314567	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56403068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57173983	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59651914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59716163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60378307	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61512578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61748068	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs728167	1.00[MKK][hapmap]
rs7295408	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7314150	0.92[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7485127	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9788014	1.00[MKK][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	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:104202200-104218200	Weak transcription	Gastric	stomach
3	chr12:104208200-104221800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:104208200-104223200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:104208200-104227800	Weak transcription	Pancreas	Pancrea
6	chr12:104208600-104221200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:104208800-104227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:104212000-104218200	Enhancers	Colon Smooth Muscle	Colon
9	chr12:104213600-104218000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:104213800-104218800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:104214800-104219400	Weak transcription	Ovary	ovary
12	chr12:104215000-104219800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:104215200-104217800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:104215200-104218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:104215200-104218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:104215200-104221800	Weak transcription	Aorta	Aorta
17	chr12:104215200-104226000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:104215400-104218600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:104215400-104221200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:104215400-104221600	Weak transcription	HepG2	liver
24	chr12:104215400-104221800	Weak transcription	Brain Angular Gyrus	brain
25	chr12:104215400-104223400	Enhancers	Rectal Smooth Muscle	rectum
26	chr12:104215800-104218400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:104215800-104218400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:104215800-104219400	Weak transcription	A549	lung
29	chr12:104215800-104221600	Weak transcription	NHLF	lung
30	chr12:104216000-104217800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:104216400-104221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:104216400-104221600	Weak transcription	HSMM	muscle
33	chr12:104216600-104217800	Weak transcription	K562	blood
34	chr12:104216600-104218200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:104216600-104219400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:104216600-104221600	Weak transcription	HMEC	breast
37	chr12:104216600-104221800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:104216600-104221800	Weak transcription	NHEK	skin
39	chr12:104216600-104227800	Weak transcription	NH-A	brain
40	chr12:104216800-104218600	Weak transcription	Osteobl	bone
41	chr12:104217000-104221400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:104217200-104218000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:104217400-104219000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:104217600-104217800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:104217600-104217800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr12:104217600-104217800	Enhancers	Fetal Muscle Leg	muscle
47	chr12:104217600-104218800	Enhancers	Psoas Muscle	Psoas
48	chr12:104217600-104219000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:104217600-104219600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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