Variant report

Variant	rs10991677
Chromosome Location	chr9:108271902-108271903
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1048215	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10491809	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.81[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816281	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816283	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10816285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816286	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10816287	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816288	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816289	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820804	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820811	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[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];1.00[ASN][1000 genomes]
rs10820815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978169	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10978172	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10978176	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978177	0.89[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978179	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991659	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10991673	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11562356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12336250	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12336844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.91[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];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12337780	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12345599	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12352975	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327352	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1327355	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1887367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296750	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297023	0.82[ASN][1000 genomes]
rs2417625	0.89[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28542455	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28851907	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750500	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793639	0.80[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3818598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55798036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023302	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7033138	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7033165	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7034149	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7037104	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7037141	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7037218	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7038407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7045862	0.80[YRI][hapmap]
rs7047791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72744263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852541	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7854411	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]
rs7856617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857186	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	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
2	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
3	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
4	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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
3	chr9:108222200-108277000	Weak transcription	Ovary	ovary
4	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
5	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:108233600-108272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:108233600-108272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:108233600-108277000	Weak transcription	Adipose Nuclei	Adipose
10	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
11	chr9:108248000-108276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:108251600-108272000	Weak transcription	HMEC	breast
13	chr9:108258200-108277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:108258200-108282000	Weak transcription	Psoas Muscle	Psoas
15	chr9:108258400-108276800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:108258400-108276800	Weak transcription	Brain Germinal Matrix	brain
17	chr9:108259000-108277000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:108259600-108272200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:108259600-108282000	Weak transcription	HSMMtube	muscle
20	chr9:108262800-108277000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:108262800-108277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:108263000-108277400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:108264000-108275000	Weak transcription	Primary B cells from cord blood	blood
24	chr9:108264800-108277000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:108265400-108277000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:108265600-108276800	Weak transcription	Dnd41	blood
27	chr9:108266200-108277400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:108266400-108275600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:108266400-108277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:108266600-108272000	Weak transcription	NHEK	skin
31	chr9:108266600-108275400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr9:108266600-108278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:108266600-108278000	Weak transcription	K562	blood
34	chr9:108266600-108282000	Weak transcription	Hela-S3	cervix
35	chr9:108266800-108277000	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:108266800-108277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:108268000-108272800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:108268000-108277200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:108268000-108277200	Weak transcription	Right Ventricle	heart
40	chr9:108268200-108277200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:108268200-108277400	Weak transcription	Fetal Brain Male	brain
42	chr9:108268200-108279000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:108268200-108279600	Weak transcription	Fetal Kidney	kidney
44	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
45	chr9:108268800-108272000	Strong transcription	HSMM	muscle
46	chr9:108269200-108273000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr9:108269200-108277000	Weak transcription	Fetal Intestine Small	intestine
48	chr9:108269200-108282000	Weak transcription	Pancreas	Pancrea
49	chr9:108269400-108277200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:108269400-108280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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