Variant report

Variant	rs7854411
Chromosome Location	chr9:108248712-108248713
allele	G/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:57)

rs_ID	r²[population]
rs1048215	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10491809	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816281	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816283	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816286	0.84[EUR][1000 genomes]
rs10816287	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816288	0.85[EUR][1000 genomes]
rs10816289	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820804	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10820811	0.91[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10820814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10820815	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10978169	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978172	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10978176	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978177	0.89[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978179	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991659	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10991673	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10991677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10991679	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11562356	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12336250	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12337780	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12345599	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12352975	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1327352	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1327355	1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1887367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296750	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297023	0.84[ASN][1000 genomes]
rs2417625	0.89[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28542455	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28851907	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750500	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3793639	0.80[ASW][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55798036	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7023302	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023520	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7033138	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7033165	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7034149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037104	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7037141	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7037218	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7038407	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045862	0.80[YRI][hapmap]
rs7047791	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72744263	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72744264	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7852541	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7856617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.95[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];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7857186	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs997319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
5	chr9:108221000-108266000	Weak transcription	NHEK	skin
6	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
7	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:108222200-108277000	Weak transcription	Ovary	ovary
9	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
10	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
11	chr9:108223200-108252600	Weak transcription	K562	blood
12	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:108228000-108258800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:108228200-108250200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:108228400-108252400	Weak transcription	Fetal Intestine Large	intestine
19	chr9:108228400-108257600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:108231400-108250200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:108231400-108257000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:108231600-108249800	Weak transcription	NHLF	lung
23	chr9:108231800-108254400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:108232000-108252200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:108232400-108249400	Weak transcription	HMEC	breast
27	chr9:108232400-108249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:108232600-108268800	Weak transcription	Fetal Brain Female	brain
29	chr9:108233000-108255000	Weak transcription	Dnd41	blood
30	chr9:108233400-108253000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:108233400-108253000	Weak transcription	Hela-S3	cervix
32	chr9:108233600-108250200	Weak transcription	A549	lung
33	chr9:108233600-108250400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:108233600-108269200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:108233600-108272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:108233600-108272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:108233600-108277000	Weak transcription	Adipose Nuclei	Adipose
38	chr9:108233800-108249600	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:108235400-108250200	Weak transcription	HSMM	muscle
40	chr9:108235800-108249000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:108236400-108259000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:108237800-108250200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:108237800-108259200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:108238800-108250000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:108239000-108253800	Weak transcription	NHDF-Ad	bronchial
46	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
47	chr9:108243400-108250600	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:108243400-108250600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr9:108243400-108252400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:108244400-108250800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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