Variant report

Variant	rs10477933
Chromosome Location	chr5:108107752-108107753
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	chr5:108106093..108108803-chr5:108119680..108121603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249921	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10035944	0.86[EUR][1000 genomes]
rs10036583	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10037675	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10039951	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10040085	0.94[EUR][1000 genomes]
rs10041657	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10041659	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042152	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10042569	0.82[CHD][hapmap]
rs10050490	0.83[EUR][1000 genomes]
rs10050547	0.86[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10052208	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10052531	0.86[ASW][hapmap];0.89[CEU][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10054086	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs10058035	0.82[EUR][1000 genomes]
rs10061362	0.87[EUR][1000 genomes]
rs10062211	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10064960	0.86[ASW][hapmap];0.89[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10065611	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10067117	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070327	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10075620	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078143	0.86[EUR][1000 genomes]
rs10477428	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10477429	0.86[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10477430	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10477432	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10477931	0.84[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10477932	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477934	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10477935	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12719099	0.86[ASW][hapmap];0.91[CHD][hapmap];0.80[TSI][hapmap]
rs13178668	0.93[ASN][1000 genomes]
rs13354622	0.94[EUR][1000 genomes]
rs13355571	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13358881	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs13359423	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs13360253	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1396444	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1423459	0.86[ASW][hapmap];0.83[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs17161505	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17161540	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1961616	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2009646	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2081127	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2081128	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2113001	0.86[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2229085	0.86[ASW][hapmap];0.91[CHD][hapmap];0.80[TSI][hapmap]
rs28521452	0.83[EUR][1000 genomes]
rs28536717	0.83[EUR][1000 genomes]
rs28611371	0.81[EUR][1000 genomes]
rs28612304	0.83[EUR][1000 genomes]
rs28633642	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28765243	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28862652	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2900036	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2900037	0.86[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35141056	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs3805598	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3805599	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41508849	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4358573	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs4361568	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs4448048	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479887	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4537096	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4560594	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHD][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs4560595	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs5019041	0.85[EUR][1000 genomes]
rs56985651	0.87[EUR][1000 genomes]
rs57561676	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57703314	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57719993	0.87[EUR][1000 genomes]
rs57908514	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57928004	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58193244	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58304901	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58530168	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59297048	0.94[EUR][1000 genomes]
rs59821709	0.87[EUR][1000 genomes]
rs60126805	0.83[EUR][1000 genomes]
rs60618804	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61170909	0.83[EUR][1000 genomes]
rs62360777	0.84[EUR][1000 genomes]
rs62360778	0.83[EUR][1000 genomes]
rs62360779	0.82[EUR][1000 genomes]
rs62360783	0.87[EUR][1000 genomes]
rs62360784	0.87[EUR][1000 genomes]
rs62360790	0.87[EUR][1000 genomes]
rs62360791	0.87[EUR][1000 genomes]
rs62360793	0.83[EUR][1000 genomes]
rs62360824	0.83[EUR][1000 genomes]
rs62360827	0.83[EUR][1000 genomes]
rs62361335	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361336	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361337	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361338	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62361341	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62361342	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62361343	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62361344	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62361345	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62363280	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62363281	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62363283	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62363284	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62363285	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62363287	0.94[EUR][1000 genomes]
rs62363289	0.89[EUR][1000 genomes]
rs62363290	0.94[EUR][1000 genomes]
rs6594341	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6594342	0.87[EUR][1000 genomes]
rs6863046	0.94[EUR][1000 genomes]
rs6873917	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6874497	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6874773	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6874968	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6875158	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6876542	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6876606	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6881932	0.86[EUR][1000 genomes]
rs6888173	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6889995	0.87[EUR][1000 genomes]
rs6890301	0.87[EUR][1000 genomes]
rs6890309	0.94[EUR][1000 genomes]
rs6894386	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7709144	0.91[CHD][hapmap]
rs7715658	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7716358	0.86[EUR][1000 genomes]
rs7719821	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs7724385	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7728920	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs889269	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs9326749	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9326750	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs9326751	0.84[EUR][1000 genomes]
rs9326752	0.86[ASW][hapmap];0.83[CEU][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9885265	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9885428	0.86[AMR][1000 genomes];0.95[EUR][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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108085600-108119800	Weak transcription	Left Ventricle	heart
2	chr5:108086200-108119200	Weak transcription	Fetal Kidney	kidney
3	chr5:108086200-108120600	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:108089800-108119400	Weak transcription	Hela-S3	cervix
5	chr5:108089800-108119800	Weak transcription	HSMM	muscle
6	chr5:108090000-108109800	Weak transcription	Adipose Nuclei	Adipose
7	chr5:108090200-108127600	Weak transcription	NH-A	brain
8	chr5:108095000-108122600	Weak transcription	Right Ventricle	heart
9	chr5:108095600-108119400	Weak transcription	Aorta	Aorta
10	chr5:108096000-108119600	Weak transcription	Primary B cells from cord blood	blood
11	chr5:108096200-108109600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:108096200-108119800	Weak transcription	HSMMtube	muscle
13	chr5:108096400-108108400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:108096400-108109200	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:108096400-108109400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:108096400-108110400	Weak transcription	Fetal Brain Female	brain
17	chr5:108096400-108112800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:108096400-108134000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:108096600-108109600	Weak transcription	Fetal Intestine Small	intestine
20	chr5:108096600-108119400	Weak transcription	Primary T cells from cord blood	blood
21	chr5:108096800-108109000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr5:108098400-108111600	Weak transcription	Brain Angular Gyrus	brain
23	chr5:108098400-108128000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:108098600-108107800	Weak transcription	Brain Substantia Nigra	brain
25	chr5:108099200-108114600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:108099200-108119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:108099200-108119400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:108099200-108119800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:108099400-108108200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr5:108099400-108119200	Weak transcription	A549	lung
31	chr5:108099400-108122400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:108099600-108117200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:108099600-108119400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:108100800-108119400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:108101400-108113000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:108101600-108117600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:108101600-108119600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:108101600-108127600	Weak transcription	Osteobl	bone
39	chr5:108101800-108109600	Weak transcription	Brain Germinal Matrix	brain
40	chr5:108101800-108117200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:108102400-108108200	Weak transcription	Fetal Heart	heart
42	chr5:108102600-108119800	Weak transcription	Pancreas	Pancrea
43	chr5:108102800-108119400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:108103000-108108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:108103000-108108400	Weak transcription	Placenta	Placenta
46	chr5:108103000-108113000	Weak transcription	NHEK	skin
47	chr5:108103000-108119400	Weak transcription	Lung	lung
48	chr5:108103400-108119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:108103600-108109000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:108104000-108108200	Weak transcription	K562	blood

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