Variant report

Variant	rs11099672
Chromosome Location	chr4:148827973-148827974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10000278	0.85[EUR][1000 genomes]
rs10001688	0.85[EUR][1000 genomes]
rs10001756	0.90[EUR][1000 genomes]
rs10003507	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10004138	1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs10004691	0.92[EUR][1000 genomes]
rs10004792	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10014593	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10014696	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10015875	0.90[EUR][1000 genomes]
rs10018820	1.00[CEU][hapmap]
rs10018903	0.82[CEU][hapmap]
rs10025069	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[EUR][1000 genomes]
rs10026985	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs10030358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10049932	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099671	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs11734553	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735412	1.00[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs12331562	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12509618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12513192	1.00[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs12641291	0.82[CEU][hapmap]
rs12643550	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650219	0.82[CEU][hapmap]
rs13129325	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13151898	0.92[EUR][1000 genomes]
rs1369958	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17024037	1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs17613979	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17614025	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17676080	1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs2043643	0.92[EUR][1000 genomes]
rs2043644	0.82[CEU][hapmap]
rs2043645	0.92[EUR][1000 genomes]
rs2118033	0.85[MEX][hapmap]
rs28576385	0.90[EUR][1000 genomes]
rs28614116	0.92[EUR][1000 genomes]
rs2884400	0.94[EUR][1000 genomes]
rs34970355	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35243600	0.92[EUR][1000 genomes]
rs35810358	0.87[EUR][1000 genomes]
rs35899247	0.92[EUR][1000 genomes]
rs3893175	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs3990920	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs4240338	0.82[CEU][hapmap]
rs4240339	0.82[CEU][hapmap]
rs4240341	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs4491995	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4571312	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs4627844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835103	0.82[CEU][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs4835109	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[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]
rs4835110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835468	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4835469	0.82[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55650760	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55820558	0.92[EUR][1000 genomes]
rs62330732	0.91[EUR][1000 genomes]
rs62330735	0.91[EUR][1000 genomes]
rs62330737	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62332176	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6535569	0.82[EUR][1000 genomes]
rs6811769	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6818371	1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs6832527	0.81[EUR][1000 genomes]
rs6840771	1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs6843392	1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs6856273	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7656471	0.82[EUR][1000 genomes]
rs7660508	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs7666127	1.00[CEU][hapmap]
rs7677632	0.92[EUR][1000 genomes]
rs7698670	0.91[EUR][1000 genomes]
rs893022	0.82[CEU][hapmap]
rs893033	1.00[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs9991741	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs9994650	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs9995896	0.82[CEU][hapmap]
rs9995956	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9996108	0.82[CEU][hapmap]
rs9997027	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9999321	0.85[EUR][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	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
2	chr4:148796800-148863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:148796800-148866000	Weak transcription	Thymus	Thymus
4	chr4:148797000-148834200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:148797000-148835800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:148797400-148879600	Weak transcription	Gastric	stomach
7	chr4:148801800-148830200	Weak transcription	NHEK	skin
8	chr4:148804600-148854400	Weak transcription	Psoas Muscle	Psoas
9	chr4:148810600-148829800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:148820600-148833400	Weak transcription	Left Ventricle	heart
11	chr4:148820600-148861200	Weak transcription	Esophagus	oesophagus
12	chr4:148820800-148848800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:148823400-148836600	Weak transcription	Placenta	Placenta
14	chr4:148823600-148831600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:148823600-148833400	Weak transcription	Fetal Stomach	stomach
16	chr4:148823600-148833800	Weak transcription	NHLF	lung
17	chr4:148823600-148834600	Weak transcription	Fetal Intestine Large	intestine
18	chr4:148824400-148828400	Weak transcription	Aorta	Aorta
19	chr4:148824400-148830200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:148824400-148831000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:148824400-148842800	Weak transcription	Lung	lung
22	chr4:148824400-148854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:148824600-148854400	Weak transcription	Right Ventricle	heart
24	chr4:148824800-148833400	Weak transcription	Fetal Intestine Small	intestine
25	chr4:148825000-148834000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:148825000-148836200	Weak transcription	HMEC	breast
27	chr4:148825200-148830200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:148825200-148831600	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:148825200-148834000	Weak transcription	NHDF-Ad	bronchial
30	chr4:148825200-148835400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:148825200-148839600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr4:148825200-148847400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:148825200-148848400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:148825400-148828000	Weak transcription	Ovary	ovary
35	chr4:148825400-148828200	Weak transcription	Adipose Nuclei	Adipose
36	chr4:148825400-148828600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:148825400-148829800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:148825400-148830000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:148825400-148830000	Weak transcription	GM12878-XiMat	blood
40	chr4:148825400-148832000	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:148825400-148832400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:148825400-148834000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:148825400-148834000	Weak transcription	Osteobl	bone
44	chr4:148825400-148843400	Weak transcription	Fetal Heart	heart
45	chr4:148825400-148844200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:148825400-148846200	Weak transcription	Fetal Kidney	kidney
47	chr4:148825400-148861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:148825400-148865800	Weak transcription	Fetal Lung	lung
49	chr4:148825800-148829400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus

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