Variant report

Variant	rs4646886
Chromosome Location	chr1:165658091-165658092
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165656454..165659398-chr1:165666338..165668915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215838	Chromatin interaction
ENSG00000143149	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10753687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753688	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs10753689	0.81[CEU][hapmap]
rs10800127	1.00[JPT][hapmap]
rs10800128	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800129	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800130	0.94[EUR][1000 genomes]
rs10800131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918241	0.96[CEU][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10918244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143659	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11506	1.00[JPT][hapmap]
rs11800476	1.00[JPT][hapmap]
rs11807857	1.00[ASN][1000 genomes]
rs12565874	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337442	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337443	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913844	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970286	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2348734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882006	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247362	0.89[EUR][1000 genomes]
rs3738192	0.94[EUR][1000 genomes]
rs3845537	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267568	1.00[ASN][1000 genomes]
rs41326750	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4233407	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646881	1.00[ASN][1000 genomes]
rs4646887	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646888	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646891	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656457	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657462	0.85[AFR][1000 genomes]
rs7368130	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543204	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7546084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555268	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555787	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS 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	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4646886	TOMM40L	cis	parietal	SCAN
rs4646886	ALDH9A1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:165638600-165665400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:165639200-165659800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:165644800-165658800	Strong transcription	HSMM	muscle
6	chr1:165645000-165660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:165647800-165658400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:165650000-165666800	Weak transcription	Colonic Mucosa	Colon
9	chr1:165651600-165659600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:165651600-165665400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:165651600-165667200	Weak transcription	Gastric	stomach
12	chr1:165651800-165665200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:165651800-165665200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:165651800-165665400	Weak transcription	Small Intestine	intestine
15	chr1:165652000-165664000	Weak transcription	Fetal Brain Male	brain
16	chr1:165652200-165665400	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:165652200-165665800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:165652200-165666000	Weak transcription	Fetal Kidney	kidney
19	chr1:165652200-165666800	Weak transcription	Lung	lung
20	chr1:165652400-165658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:165652400-165659200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:165652400-165659400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:165652400-165659600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:165652400-165659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:165652400-165659600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:165652400-165659600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:165652400-165659800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:165652400-165665200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:165652400-165665400	Weak transcription	HMEC	breast
30	chr1:165652400-165665400	Weak transcription	NH-A	brain
31	chr1:165652400-165665800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:165652400-165665800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:165652400-165665800	Weak transcription	HSMMtube	muscle
34	chr1:165652400-165666800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:165652400-165666800	Weak transcription	Esophagus	oesophagus
36	chr1:165652400-165667000	Weak transcription	Pancreas	Pancrea
37	chr1:165652400-165667000	Weak transcription	Spleen	Spleen
38	chr1:165652600-165666000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:165652800-165665400	Weak transcription	NHLF	lung
40	chr1:165652800-165666200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:165653000-165666000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:165653400-165658800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:165653400-165659800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:165653800-165659800	Weak transcription	Brain Germinal Matrix	brain
45	chr1:165653800-165665200	Weak transcription	NHEK	skin
46	chr1:165653800-165666000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:165654000-165659600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:165654000-165660000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:165654000-165661400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:165654400-165658200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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