Variant report

Variant	rs9828899
Chromosome Location	chr3:110803025-110803026
allele	C/T
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]
rs11717706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.83[JPT][hapmap]
rs13060876	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061640	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13072462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][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];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]
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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[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];1.00[LWK][hapmap];1.00[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];0.97[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]
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];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[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];1.00[ASN][1000 genomes]
rs2169643	0.85[CEU][hapmap]
rs2399373	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]
rs2399375	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[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];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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682230	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682234	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];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];0.85[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];0.82[ASN][1000 genomes]
rs6437948	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];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6437952	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs6437955	0.80[AMR][1000 genomes]
rs66803420	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67209183	0.80[ASN][1000 genomes]
rs6763050	0.85[CEU][hapmap]
rs6765133	0.83[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];1.00[ASN][1000 genomes]
rs7612667	0.82[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];0.94[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];1.00[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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][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];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.99[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];1.00[ASN][1000 genomes]
rs9826064	0.81[AFR][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];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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110792600-110803600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:110794200-110809200	Weak transcription	Fetal Brain Male	brain
3	chr3:110794400-110813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:110794800-110804600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:110794800-110805200	Enhancers	Dnd41	blood
6	chr3:110796000-110804600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:110796200-110806800	Weak transcription	Small Intestine	intestine
8	chr3:110796600-110803600	Weak transcription	HepG2	liver
9	chr3:110798800-110803600	Weak transcription	Fetal Intestine Large	intestine
10	chr3:110799000-110807000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:110799000-110807000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:110799800-110820600	Weak transcription	A549	lung
13	chr3:110800000-110803200	Weak transcription	Fetal Intestine Small	intestine
14	chr3:110800000-110803600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:110800000-110804200	Weak transcription	Stomach Mucosa	stomach
16	chr3:110800200-110803800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:110800200-110812400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:110800200-110817200	Weak transcription	Gastric	stomach
19	chr3:110800400-110803800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:110800400-110804200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:110800600-110803400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:110800600-110803800	Weak transcription	Osteobl	bone
23	chr3:110800800-110803600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:110800800-110803800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:110800800-110804400	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:110801000-110803800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:110801000-110803800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:110801000-110804200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:110801000-110804600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:110801200-110803400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:110801200-110803800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:110801200-110803800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:110801200-110804400	Weak transcription	Fetal Lung	lung
34	chr3:110801800-110804600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:110802000-110803200	Weak transcription	Liver	Liver
36	chr3:110802000-110822600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:110802200-110803400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:110802400-110806600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:110802400-110806600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:110802600-110803800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:110802600-110803800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:110802800-110804400	Enhancers	NHDF-Ad	bronchial
43	chr3:110802800-110804600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:110802800-110805600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:110802800-110806800	Weak transcription	Ovary	ovary

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