Variant report

Variant	rs1477843
Chromosome Location	chr3:110829907-110829908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11717706	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919892	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11929280	0.85[CEU][hapmap]
rs12492309	0.83[JPT][hapmap]
rs13060876	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061640	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13072462	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382075	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1477841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1477842	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs1477846	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1477847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.86[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs1477854	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1477855	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1547518	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1585629	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1600059	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1871026	0.88[AFR][1000 genomes]
rs2126710	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2126711	0.89[EUR][1000 genomes]
rs2126712	0.89[EUR][1000 genomes]
rs2126713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169643	0.85[CEU][hapmap]
rs2399373	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]
rs2399375	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682034	0.80[AMR][1000 genomes]
rs4682229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[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]
rs4682231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4682234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682238	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6437947	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6437948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6437952	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs6437955	0.83[AMR][1000 genomes]
rs66803420	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67209183	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6765133	0.83[JPT][hapmap]
rs6765948	0.81[EUR][1000 genomes]
rs6781480	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6790828	0.81[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];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7433877	0.85[CEU][hapmap]
rs7610760	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs7612572	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612667	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623847	0.80[AMR][1000 genomes]
rs7623880	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7632375	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7632388	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7648752	0.82[CEU][hapmap]
rs7653595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs873132	0.85[CEU][hapmap]
rs9288918	0.85[CEU][hapmap]
rs9818950	0.89[EUR][1000 genomes]
rs9821335	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[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];1.00[ASN][1000 genomes]
rs9837377	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9847598	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9866028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877855	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9882945	0.85[CEU][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	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
5	nsv591276	chr3:110822496-110854196	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv877338	chr3:110824425-110860188	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110805000-110833600	Weak transcription	NHDF-Ad	bronchial
2	chr3:110816000-110837600	Weak transcription	Fetal Stomach	stomach
3	chr3:110816000-110873800	Weak transcription	Left Ventricle	heart
4	chr3:110816000-110893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:110817400-110855200	Weak transcription	Pancreas	Pancrea
6	chr3:110817600-110837600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:110819200-110857200	Weak transcription	NHLF	lung
8	chr3:110823400-110838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:110823400-110838000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:110824200-110832200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:110826400-110830400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:110826600-110831800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:110826600-110845000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:110826800-110831800	Weak transcription	Fetal Lung	lung
15	chr3:110826800-110847600	Weak transcription	A549	lung
16	chr3:110826800-110884200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:110827000-110847400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:110827600-110831600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:110827600-110831800	Weak transcription	Dnd41	blood
20	chr3:110827600-110831800	Weak transcription	HSMMtube	muscle
21	chr3:110827600-110833400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:110827600-110842200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:110827800-110830200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:110827800-110831000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:110827800-110849200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:110828000-110830400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:110828000-110830400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:110828000-110830400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:110828000-110830400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:110828000-110830400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:110828000-110830400	Weak transcription	Psoas Muscle	Psoas
32	chr3:110828000-110830600	Weak transcription	Ovary	ovary
33	chr3:110828000-110831800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:110828000-110831800	Weak transcription	Small Intestine	intestine
35	chr3:110828000-110837200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:110828000-110851400	Weak transcription	Aorta	Aorta
37	chr3:110828200-110830400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:110828800-110830400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:110829400-110893400	Weak transcription	HUVEC	blood vessel
40	chr3:110829600-110830800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr3:110829600-110837600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:110829800-110831400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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