Variant report

Variant	rs2439232
Chromosome Location	chr3:98566671-98566672
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10428160	0.85[EUR][1000 genomes]
rs10589669	0.89[EUR][1000 genomes]
rs11552978	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs12107272	0.89[EUR][1000 genomes]
rs12108018	0.91[EUR][1000 genomes]
rs13059624	0.89[CEU][hapmap];1.00[GIH][hapmap]
rs13065136	0.89[EUR][1000 genomes]
rs13068317	0.87[EUR][1000 genomes]
rs13074614	0.91[EUR][1000 genomes]
rs13074787	0.85[EUR][1000 genomes]
rs13076960	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs13078549	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13081992	0.89[EUR][1000 genomes]
rs13083238	0.91[EUR][1000 genomes]
rs13083613	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13083934	0.91[EUR][1000 genomes]
rs13084692	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs13087627	0.89[EUR][1000 genomes]
rs13087631	0.91[EUR][1000 genomes]
rs13088532	0.81[EUR][1000 genomes]
rs13091170	0.89[EUR][1000 genomes]
rs13091236	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs13093128	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13096085	0.89[EUR][1000 genomes]
rs13097876	0.89[EUR][1000 genomes]
rs13100915	0.89[EUR][1000 genomes]
rs13100937	0.89[EUR][1000 genomes]
rs1818053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2439234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2454687	0.98[EUR][1000 genomes]
rs2454690	1.00[ASN][1000 genomes]
rs2470858	0.80[ASN][1000 genomes]
rs2470874	1.00[ASN][1000 genomes]
rs278377	1.00[ASN][1000 genomes]
rs34008360	0.91[EUR][1000 genomes]
rs34269725	0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[EUR][1000 genomes]
rs34279227	0.91[EUR][1000 genomes]
rs34284740	0.89[EUR][1000 genomes]
rs34394867	0.85[EUR][1000 genomes]
rs34428696	0.87[EUR][1000 genomes]
rs34489202	0.89[EUR][1000 genomes]
rs34688367	0.91[EUR][1000 genomes]
rs34711372	0.91[EUR][1000 genomes]
rs34725039	0.89[EUR][1000 genomes]
rs34826460	0.89[EUR][1000 genomes]
rs34848749	0.91[EUR][1000 genomes]
rs34860591	0.89[EUR][1000 genomes]
rs35006699	0.91[EUR][1000 genomes]
rs35025156	0.89[EUR][1000 genomes]
rs35076733	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35098355	0.91[EUR][1000 genomes]
rs35103318	0.89[EUR][1000 genomes]
rs35219252	0.91[EUR][1000 genomes]
rs35234681	0.87[EUR][1000 genomes]
rs35239055	0.91[EUR][1000 genomes]
rs35312318	0.89[EUR][1000 genomes]
rs35366262	0.91[EUR][1000 genomes]
rs35422064	0.91[EUR][1000 genomes]
rs35499232	0.89[EUR][1000 genomes]
rs35514544	0.89[EUR][1000 genomes]
rs35526367	0.85[EUR][1000 genomes]
rs35539438	0.89[EUR][1000 genomes]
rs35592768	0.85[EUR][1000 genomes]
rs35764973	0.89[EUR][1000 genomes]
rs35914268	0.91[EUR][1000 genomes]
rs35947806	0.91[EUR][1000 genomes]
rs36098932	0.89[EUR][1000 genomes]
rs36157152	0.89[EUR][1000 genomes]
rs55644421	0.91[EUR][1000 genomes]
rs56083233	0.89[EUR][1000 genomes]
rs56246599	0.89[EUR][1000 genomes]
rs56408882	0.85[EUR][1000 genomes]
rs6764579	0.87[EUR][1000 genomes]
rs6805362	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs71311397	0.81[EUR][1000 genomes]
rs71311398	0.91[EUR][1000 genomes]
rs71311402	0.91[EUR][1000 genomes]
rs71313504	0.89[EUR][1000 genomes]
rs71313506	0.96[EUR][1000 genomes]
rs71313508	0.89[EUR][1000 genomes]
rs71313509	0.89[EUR][1000 genomes]
rs71313510	0.89[EUR][1000 genomes]
rs71313511	0.89[EUR][1000 genomes]
rs7614053	0.91[EUR][1000 genomes]
rs7621508	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs828606	0.84[YRI][hapmap]
rs828622	1.00[ASN][1000 genomes]
rs866873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9883226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs996199	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:98536200-98594200	Weak transcription	HepG2	liver
4	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98537000-98592800	Weak transcription	K562	blood
6	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:98541200-98567000	Weak transcription	Liver	Liver
8	chr3:98550200-98568600	Weak transcription	Thymus	Thymus
9	chr3:98552600-98567000	Weak transcription	Fetal Kidney	kidney
10	chr3:98552800-98575800	Weak transcription	Pancreas	Pancrea
11	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
13	chr3:98553000-98566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:98553000-98566800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:98553000-98567000	Weak transcription	Brain Germinal Matrix	brain
16	chr3:98553000-98575600	Weak transcription	Fetal Stomach	stomach
17	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
19	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:98558200-98566800	Weak transcription	Fetal Thymus	thymus
21	chr3:98558200-98569400	Weak transcription	Fetal Intestine Large	intestine
22	chr3:98558200-98569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:98558200-98577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:98558400-98568800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:98558800-98567000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:98559000-98567000	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:98559000-98569000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:98559600-98576800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:98559800-98566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:98559800-98567000	Weak transcription	Dnd41	blood
31	chr3:98559800-98569400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:98560000-98566800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:98560000-98575600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:98560200-98566800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:98560200-98567000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:98560200-98575800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:98561200-98567000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:98561600-98567600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:98562400-98575600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:98563000-98567000	Weak transcription	Fetal Lung	lung
41	chr3:98563000-98574400	Weak transcription	HSMMtube	muscle
42	chr3:98563200-98569000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:98563400-98568800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:98563600-98576000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:98563800-98569200	Strong transcription	NHEK	skin
46	chr3:98564200-98569800	Strong transcription	HMEC	breast
47	chr3:98564600-98566800	Genic enhancers	NH-A	brain
48	chr3:98564600-98567000	Weak transcription	Psoas Muscle	Psoas
49	chr3:98564600-98574800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:98565000-98566800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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