Variant report

Variant	rs2309647
Chromosome Location	chr9:72841914-72841915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10119662	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10125617	0.86[JPT][hapmap]
rs1052684	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10780923	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868720	0.91[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs10868752	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10868757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868775	0.83[EUR][1000 genomes]
rs10868799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868801	0.86[JPT][hapmap]
rs10868806	0.85[JPT][hapmap]
rs11142350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[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];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1536956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927099	0.84[EUR][1000 genomes]
rs1927102	0.84[EUR][1000 genomes]
rs1927128	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1927139	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2026136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2182736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2210086	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2309611	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309612	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309633	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2309642	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3847321	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3858107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[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];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744990	0.85[ASN][1000 genomes]
rs4745000	0.85[JPT][hapmap]
rs6560019	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6560127	0.82[EUR][1000 genomes]
rs7021420	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7027209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[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];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7043043	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7469211	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7866915	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9650766	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72793000-72842600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72821200-72844800	Weak transcription	HMEC	breast
3	chr9:72827600-72843200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:72828000-72844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:72828000-72858800	Weak transcription	Gastric	stomach
6	chr9:72828200-72843200	Weak transcription	Fetal Lung	lung
7	chr9:72828200-72844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:72828600-72843000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:72829600-72843400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:72830800-72845200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:72832400-72848800	Weak transcription	Lung	lung
12	chr9:72833600-72856800	Weak transcription	Aorta	Aorta
13	chr9:72834400-72843800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:72834600-72844000	Weak transcription	Left Ventricle	heart
15	chr9:72835600-72842400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:72835600-72843200	Weak transcription	Ovary	ovary
17	chr9:72835800-72843200	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:72836800-72842400	Weak transcription	Adipose Nuclei	Adipose
19	chr9:72837200-72847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:72837800-72843200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:72837800-72844000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:72838200-72843600	Weak transcription	Osteobl	bone
23	chr9:72838400-72842400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:72839800-72844800	Weak transcription	HSMMtube	muscle
25	chr9:72840400-72843200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:72840400-72844000	Weak transcription	HSMM	muscle
27	chr9:72841200-72843800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:72841400-72843400	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:72841400-72844200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:72841600-72843200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:72841600-72843200	Weak transcription	Stomach Smooth Muscle	stomach

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