Variant report

Variant	rs12617761
Chromosome Location	chr2:20088018-20088019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20085889..20088843-chr2:20102352..20104719,3	MCF-7	breast:
2	chr2:20070422..20073365-chr2:20086034..20088934,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10169398	0.87[JPT][hapmap];1.00[MEX][hapmap]
rs10197385	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs10204428	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs10495701	0.87[CEU][hapmap];1.00[MEX][hapmap]
rs1060742	0.87[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs11096632	0.87[CEU][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs11888045	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11889206	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12052274	0.81[ASN][1000 genomes]
rs12613209	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs12620863	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs13421472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381817	0.87[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs16987265	0.87[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs2293671	0.87[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs2304588	0.87[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs28502265	0.81[ASN][1000 genomes]
rs35957485	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62109397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109398	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109404	0.83[ASN][1000 genomes]
rs62109406	0.81[ASN][1000 genomes]
rs62109413	0.80[AMR][1000 genomes]
rs62109415	0.80[AMR][1000 genomes]
rs62109418	0.80[AMR][1000 genomes]
rs6707471	0.87[JPT][hapmap];1.00[MEX][hapmap]
rs6719397	0.87[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs7563410	0.87[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7572167	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs7594214	0.87[CEU][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12617761	LOC130502	cis	multi-tissue	Pritchard
rs12617761	TTC32	cis	lymphoblastoid	seeQTL
rs12617761	TTC32	cis	lung	GTEx
rs12617761	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs12617761	TTC32	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
2	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
3	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:20075400-20097600	Weak transcription	Fetal Kidney	kidney
5	chr2:20076400-20093600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:20076400-20097200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:20076600-20097400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:20076800-20091000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:20076800-20095400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:20076800-20095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:20076800-20097200	Weak transcription	Fetal Thymus	thymus
13	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:20079200-20098600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:20079400-20097200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:20079800-20099000	Weak transcription	Thymus	Thymus
18	chr2:20081800-20095200	Weak transcription	Primary T cells from cord blood	blood
19	chr2:20083000-20095400	Weak transcription	Fetal Brain Female	brain
20	chr2:20085600-20088600	Weak transcription	Right Ventricle	heart
21	chr2:20085800-20090000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:20086400-20097400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:20086600-20088600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:20086600-20089200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:20086600-20089200	Weak transcription	NHEK	skin
26	chr2:20086600-20091200	Weak transcription	Psoas Muscle	Psoas
27	chr2:20086600-20091800	Weak transcription	Spleen	Spleen
28	chr2:20086600-20095400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:20086600-20097400	Weak transcription	HMEC	breast
30	chr2:20086600-20099800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:20086800-20089000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:20087000-20088400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:20087000-20088400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr2:20087000-20088600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:20087200-20089200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:20087200-20097400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:20087400-20097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:20087600-20088600	Weak transcription	Brain Substantia Nigra	brain
39	chr2:20087800-20088400	Enhancers	Gastric	stomach
40	chr2:20087800-20090600	Enhancers	Left Ventricle	heart
41	chr2:20088000-20091200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:20088000-20099600	Weak transcription	Rectal Mucosa Donor 31	rectum

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