Variant report

Variant	rs2399373
Chromosome Location	chr3:110793050-110793051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10433385	0.82[CHB][hapmap]
rs11717706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11919892	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11929280	0.85[CEU][hapmap]
rs12492309	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13060876	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061640	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13093206	0.81[AFR][1000 genomes]
rs1381836	0.85[CEU][hapmap]
rs1382075	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1462789	0.81[AFR][1000 genomes]
rs1462790	0.81[AFR][1000 genomes]
rs1462795	0.81[AFR][1000 genomes]
rs1477841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1477842	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs1477843	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477846	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1477847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477848	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1477850	0.85[CEU][hapmap]
rs1477851	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1477854	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1477855	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1547518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1585629	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1600059	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16857350	0.85[CEU][hapmap]
rs1871026	0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1903755	0.81[AFR][1000 genomes]
rs2126710	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2126711	0.94[EUR][1000 genomes]
rs2126712	0.94[EUR][1000 genomes]
rs2126713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2169643	0.85[CEU][hapmap]
rs2399375	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2895376	0.80[AFR][1000 genomes]
rs4102676	0.81[AFR][1000 genomes]
rs4682033	0.82[AFR][1000 genomes]
rs4682229	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[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]
rs4682231	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs4682234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4682238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs55774570	0.82[AFR][1000 genomes]
rs56668317	0.82[AFR][1000 genomes]
rs6437940	0.81[AFR][1000 genomes]
rs6437947	0.90[AFR][1000 genomes]
rs6437948	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6437952	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs6437955	0.80[AMR][1000 genomes]
rs66803420	0.80[AMR][1000 genomes]
rs6763050	0.85[CEU][hapmap]
rs6765133	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6765948	0.86[EUR][1000 genomes]
rs6781480	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6790828	0.85[AFR][1000 genomes]
rs6794645	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7430600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7433877	0.85[CEU][hapmap]
rs7610760	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs7612572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7612667	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7623880	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7632375	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7632388	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7648752	0.82[CEU][hapmap]
rs7653595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs873132	0.85[CEU][hapmap]
rs9288918	0.85[CEU][hapmap]
rs969940	0.85[CEU][hapmap]
rs9817950	0.83[AFR][1000 genomes]
rs9818950	0.94[EUR][1000 genomes]
rs9821335	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826064	0.81[AFR][1000 genomes]
rs9828899	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[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];0.97[ASN][1000 genomes]
rs9837377	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9839674	0.81[AFR][1000 genomes]
rs9847598	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9866028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9876350	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877855	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9882945	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers 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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110788600-110794200	Active TSS	Ovary	ovary
2	chr3:110788600-110794600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:110788800-110793200	Active TSS	Fetal Kidney	kidney
4	chr3:110788800-110794000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:110789000-110793200	Active TSS	Fetal Stomach	stomach
6	chr3:110789000-110793200	Active TSS	Stomach Smooth Muscle	stomach
7	chr3:110789000-110793400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:110789000-110793600	Active TSS	NHDF-Ad	bronchial
9	chr3:110789000-110793800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:110789000-110794200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:110789200-110793200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:110789200-110793400	Active TSS	Fetal Intestine Large	intestine
13	chr3:110789200-110793600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr3:110789200-110794200	Active TSS	NHLF	lung
15	chr3:110789200-110794800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:110789400-110794000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:110789600-110794800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:110791800-110793200	Active TSS	Fetal Intestine Small	intestine
19	chr3:110791800-110793400	Active TSS	Placenta	Placenta
20	chr3:110791800-110794200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:110792000-110793400	Flanking Active TSS	HUVEC	blood vessel
22	chr3:110792200-110793200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:110792200-110793400	Flanking Active TSS	HepG2	liver
24	chr3:110792200-110794200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:110792200-110794400	Active TSS	Duodenum Mucosa	Duodenum
26	chr3:110792200-110794800	Flanking Active TSS	Dnd41	blood
27	chr3:110792400-110793200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:110792400-110793200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:110792400-110793200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:110792400-110793400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:110792400-110794000	Enhancers	Brain Hippocampus Middle	brain
32	chr3:110792400-110795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:110792400-110795600	Weak transcription	Small Intestine	intestine
34	chr3:110792600-110793200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr3:110792600-110793200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:110792600-110793200	Active TSS	Fetal Brain Male	brain
37	chr3:110792600-110793200	Enhancers	Stomach Mucosa	stomach
38	chr3:110792600-110793200	Flanking Active TSS	A549	lung
39	chr3:110792600-110793200	Enhancers	Hela-S3	cervix
40	chr3:110792600-110793600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr3:110792600-110793800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:110792600-110794200	Active TSS	NH-A	brain
43	chr3:110792600-110800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:110792600-110802200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:110792600-110803600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:110792800-110793200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:110792800-110793200	Enhancers	Brain Cingulate Gyrus	brain
48	chr3:110792800-110793200	Enhancers	Brain Germinal Matrix	brain
49	chr3:110792800-110793200	Flanking Active TSS	Fetal Lung	lung
50	chr3:110792800-110794000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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