Variant report

Variant	rs13092707
Chromosome Location	chr3:135789956-135789957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135788877..135792227-chr3:135914982..135916862,3	MCF-7	breast:
2	chr3:135788920..135791569-chr3:136470334..136472063,2	MCF-7	breast:
3	chr1:173013039..173013740-chr3:135789899..135790668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12630389	0.91[ASN][1000 genomes]
rs12632791	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12633805	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12637541	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059064	0.87[ASN][1000 genomes]
rs13065499	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13069408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13072433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13072690	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13072782	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13075579	0.97[ASN][1000 genomes]
rs13078865	0.88[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs13084404	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13097172	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13097176	0.82[ASN][1000 genomes]
rs13097267	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13100235	0.83[ASN][1000 genomes]
rs1523593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523598	0.82[ASN][1000 genomes]
rs1523599	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843560	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16843611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140450	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2177407	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2400649	0.87[ASN][1000 genomes]
rs34447526	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34683314	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34706807	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35097316	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35209948	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35264626	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35532770	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35946332	0.87[ASN][1000 genomes]
rs35961065	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3946444	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4075999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4331626	0.87[ASN][1000 genomes]
rs4678224	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4678288	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55873361	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56152207	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57594457	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60070757	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61791712	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61791714	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439603	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6439605	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6439609	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6439610	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6439614	0.86[ASN][1000 genomes]
rs6439615	0.87[ASN][1000 genomes]
rs6439618	0.87[ASN][1000 genomes]
rs6439622	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6439623	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6439624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6770366	0.84[ASN][1000 genomes]
rs6771950	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775261	0.87[ASN][1000 genomes]
rs6779903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6793273	0.87[ASN][1000 genomes]
rs6803786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7433592	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610302	0.87[ASN][1000 genomes]
rs7625177	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7625607	0.89[ASN][1000 genomes]
rs7635621	0.87[ASN][1000 genomes]
rs7650079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289501	0.85[ASN][1000 genomes]
rs940229	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9682712	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9758578	0.96[ASN][1000 genomes]
rs9846554	0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9852009	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9852169	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9856799	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs9866235	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs9868239	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS 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	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13092707	NCK1	cis	cerebellum	SCAN
rs13092707	SLC9A7	trans	cerebellum	SCAN
rs13092707	NCK1	cis	parietal	SCAN
rs13092707	TMEM22	cis	cerebellum	SCAN
rs13092707	MSL2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:135764400-135790400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:135764800-135790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
7	chr3:135768800-135800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:135769800-135790000	Weak transcription	Aorta	Aorta
9	chr3:135769800-135790400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:135770000-135800800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:135771200-135802000	Weak transcription	Brain Germinal Matrix	brain
12	chr3:135771200-135809600	Weak transcription	Gastric	stomach
13	chr3:135774400-135802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
15	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:135781400-135790400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:135781400-135801600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:135781400-135802000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:135781400-135803000	Weak transcription	Right Ventricle	heart
20	chr3:135784200-135805600	Weak transcription	Stomach Mucosa	stomach
21	chr3:135785000-135798400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:135785600-135792200	Weak transcription	Fetal Lung	lung
23	chr3:135785600-135799000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:135785600-135801800	Weak transcription	Pancreas	Pancrea
25	chr3:135787000-135790000	Enhancers	NHDF-Ad	bronchial
26	chr3:135787200-135790000	Enhancers	Osteobl	bone
27	chr3:135787400-135790800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:135787400-135791000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:135787400-135791000	Enhancers	NHLF	lung
30	chr3:135787800-135791400	Enhancers	NH-A	brain
31	chr3:135788400-135790600	Weak transcription	Fetal Kidney	kidney
32	chr3:135788600-135791200	Enhancers	HMEC	breast
33	chr3:135788800-135790000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:135788800-135790800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:135788800-135790800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:135788800-135791000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:135788800-135798600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:135789000-135790000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:135789000-135790400	Enhancers	HSMMtube	muscle
40	chr3:135789000-135790600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:135789200-135790800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:135789200-135790800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:135789200-135791000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:135789200-135791200	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:135789400-135790600	Enhancers	Colon Smooth Muscle	Colon
46	chr3:135789400-135790600	Enhancers	Stomach Smooth Muscle	stomach
47	chr3:135789400-135790800	Enhancers	Rectal Smooth Muscle	rectum
48	chr3:135789400-135791400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:135789600-135790200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:135789600-135790600	Enhancers	A549	lung

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