Variant report

Variant	rs9866028
Chromosome Location	chr3:110836281-110836282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11717706	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11929280	0.85[CEU][hapmap]
rs12492309	0.83[JPT][hapmap]
rs13060876	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061640	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13072462	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13093206	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1477841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1477842	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1477843	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]
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];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1547518	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[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];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]
rs2399375	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682033	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4682034	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs4682231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
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];0.96[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];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs55774570	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56668317	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs57417964	0.94[AFR][1000 genomes];0.86[EUR][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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437952	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6437955	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66803420	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67209183	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6765133	0.83[JPT][hapmap]
rs6786854	0.87[EUR][1000 genomes]
rs6794645	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7433877	0.85[CEU][hapmap]
rs7610760	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7612572	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7623847	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7623880	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[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];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs873132	0.85[CEU][hapmap]
rs9288918	0.85[CEU][hapmap]
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];0.90[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.89[ASN][1000 genomes]
rs9876350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882526	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9882945	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv1008308	chr3:110836281-110885834	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110816000-110837600	Weak transcription	Fetal Stomach	stomach
2	chr3:110816000-110873800	Weak transcription	Left Ventricle	heart
3	chr3:110816000-110893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:110817400-110855200	Weak transcription	Pancreas	Pancrea
5	chr3:110817600-110837600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:110819200-110857200	Weak transcription	NHLF	lung
7	chr3:110823400-110838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:110823400-110838000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:110826600-110845000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:110826800-110847600	Weak transcription	A549	lung
11	chr3:110826800-110884200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:110827000-110847400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:110827600-110842200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:110827800-110849200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:110828000-110837200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:110828000-110851400	Weak transcription	Aorta	Aorta
17	chr3:110829400-110893400	Weak transcription	HUVEC	blood vessel
18	chr3:110829600-110837600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:110830400-110852800	Weak transcription	NH-A	brain
20	chr3:110830600-110854200	Weak transcription	Right Ventricle	heart
21	chr3:110830800-110836800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:110830800-110837600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:110830800-110837600	Weak transcription	Fetal Intestine Large	intestine
24	chr3:110830800-110852400	Weak transcription	Fetal Brain Male	brain
25	chr3:110830800-110853800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:110831200-110837800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:110831600-110844000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:110831800-110842200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:110832000-110840400	Weak transcription	HSMM	muscle
30	chr3:110832000-110840800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:110832000-110854600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:110832000-110854600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:110832000-110856600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:110832200-110837200	Weak transcription	Fetal Lung	lung
35	chr3:110832200-110837400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:110832200-110840800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:110832200-110842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:110832200-110847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:110832200-110852400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:110832200-110853600	Weak transcription	HSMMtube	muscle
41	chr3:110832200-110881800	Weak transcription	Small Intestine	intestine
42	chr3:110832200-110892400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:110832400-110841800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:110832400-110911200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:110832600-110840800	Weak transcription	Placenta	Placenta
46	chr3:110832800-110852400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:110833000-110845000	Weak transcription	Fetal Kidney	kidney
48	chr3:110833200-110837200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:110833600-110855400	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:110833800-110837200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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