Variant report

Variant	rs13123618
Chromosome Location	chr4:110370867-110370868
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	chr4:110353843..110356586-chr4:110367981..110370945,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138802	Chromatin interaction
ENSG00000247950	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10000545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10002595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005355	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10016533	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10155127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10516558	0.93[CEU][hapmap];0.96[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11098033	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11098035	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11929713	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11930655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11933971	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934486	0.90[ASN][1000 genomes]
rs11935440	0.94[ASN][1000 genomes]
rs11935629	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11938593	0.94[ASN][1000 genomes]
rs11941344	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942140	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11942291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942858	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942928	0.94[ASN][1000 genomes]
rs11943384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11943430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11944375	0.94[ASN][1000 genomes]
rs11944427	0.94[ASN][1000 genomes]
rs11944659	0.90[ASN][1000 genomes]
rs12639832	0.90[ASN][1000 genomes]
rs12640049	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12640161	0.98[ASN][1000 genomes]
rs12642304	0.92[ASN][1000 genomes]
rs12643055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12643844	0.92[ASN][1000 genomes]
rs12644055	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs12647695	0.94[ASN][1000 genomes]
rs12648138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12648965	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12650654	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12650873	0.94[ASN][1000 genomes]
rs13103034	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110999	0.86[CEU][hapmap]
rs13122093	0.86[CEU][hapmap]
rs13125368	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13128124	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13128221	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs13128445	0.85[MEX][hapmap]
rs13134239	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13140373	0.86[CEU][hapmap]
rs13141701	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13142698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13143825	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13145066	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1509314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509315	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040410	0.94[ASN][1000 genomes]
rs17040436	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040439	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040461	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040488	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17040510	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17585970	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17619262	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs28521972	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28681408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34153531	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34224638	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34274964	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34377662	0.85[ASN][1000 genomes]
rs34441811	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34482781	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505473	0.90[EUR][1000 genomes]
rs34636377	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34836476	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35110951	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35359830	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35473144	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35594044	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35762958	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35791246	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940980	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36009064	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36115572	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3775962	0.92[ASN][1000 genomes]
rs60957336	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61004219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61242473	0.90[ASN][1000 genomes]
rs61439452	0.92[ASN][1000 genomes]
rs61553525	0.94[ASN][1000 genomes]
rs6533428	0.84[ASN][1000 genomes]
rs6533429	0.94[ASN][1000 genomes]
rs6533434	1.00[MEX][hapmap]
rs66642182	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66667140	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67473696	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68041341	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812469	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6817954	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6818911	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6823032	0.92[ASN][1000 genomes]
rs6825928	0.88[MEX][hapmap]
rs6827006	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833753	0.90[ASN][1000 genomes]
rs6835683	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6837199	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6841198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845371	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6848452	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6851517	0.94[ASN][1000 genomes]
rs6852037	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6856291	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6856446	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71603033	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72896619	0.98[ASN][1000 genomes]
rs72896622	0.98[ASN][1000 genomes]
rs72896625	0.98[ASN][1000 genomes]
rs72896629	0.98[ASN][1000 genomes]
rs72896632	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73838809	0.92[ASN][1000 genomes]
rs7436583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7436745	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7440371	0.94[ASN][1000 genomes]
rs7440570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7679836	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7680296	0.91[EUR][1000 genomes]
rs7687245	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9985632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9985964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9994676	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9994985	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1836921	chr4:110354632-110370867	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv1839822	chr4:110354632-110370867	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110358000-110372000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:110358000-110384000	Weak transcription	Fetal Brain Male	brain
3	chr4:110358000-110384200	Weak transcription	Colonic Mucosa	Colon
4	chr4:110358600-110378600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:110360400-110384200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:110363000-110384200	Weak transcription	Esophagus	oesophagus
7	chr4:110363600-110371000	Weak transcription	Stomach Mucosa	stomach
8	chr4:110363600-110372000	Weak transcription	K562	blood
9	chr4:110363600-110383600	Weak transcription	Pancreas	Pancrea
10	chr4:110363600-110383600	Weak transcription	NHDF-Ad	bronchial
11	chr4:110363600-110384200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:110363600-110384200	Weak transcription	Hela-S3	cervix
13	chr4:110363600-110398400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:110364600-110384200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:110365000-110372000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:110365000-110383400	Weak transcription	Fetal Heart	heart
17	chr4:110365000-110384000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:110365200-110371000	Weak transcription	NH-A	brain
19	chr4:110365200-110384200	Weak transcription	Aorta	Aorta
20	chr4:110366000-110391400	Weak transcription	Small Intestine	intestine
21	chr4:110367200-110373600	Strong transcription	NHEK	skin
22	chr4:110367200-110373800	Strong transcription	HSMM	muscle
23	chr4:110367400-110383600	Weak transcription	HUVEC	blood vessel
24	chr4:110367600-110372000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:110367600-110372400	Weak transcription	Psoas Muscle	Psoas
26	chr4:110367600-110373400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:110367600-110374200	Weak transcription	Gastric	stomach
28	chr4:110367600-110375000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:110367600-110375600	Weak transcription	Brain Substantia Nigra	brain
30	chr4:110367600-110376800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:110367600-110383200	Weak transcription	Right Ventricle	heart
32	chr4:110367600-110383800	Weak transcription	NHLF	lung
33	chr4:110367600-110384000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:110367600-110384200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:110367600-110384200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:110367600-110384200	Weak transcription	Brain Germinal Matrix	brain
37	chr4:110367800-110371000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:110367800-110371200	Weak transcription	A549	lung
39	chr4:110367800-110372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:110367800-110373400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:110367800-110375000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:110367800-110377400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:110367800-110380800	Weak transcription	Brain Angular Gyrus	brain
44	chr4:110367800-110383800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:110367800-110383800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:110367800-110384200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:110367800-110384200	Weak transcription	Fetal Kidney	kidney
48	chr4:110367800-110384200	Weak transcription	Osteobl	bone
49	chr4:110368000-110372600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:110368000-110374000	Weak transcription	Placenta	Placenta

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