Variant report

Variant	rs1571895
Chromosome Location	chr9:97788956-97788957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97783764..97786051-chr9:97788470..97790440,2	K562	blood:
2	chr9:97786821..97789606-chr9:97794967..97796572,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1004373	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10117370	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10119512	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10121760	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123819	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1020963	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][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];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10512253	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761364	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10761366	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761368	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][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];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10761369	0.83[CEU][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs10993427	0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993456	0.82[TSI][hapmap]
rs10993464	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993467	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1113102	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12339639	0.82[TSI][hapmap]
rs1412488	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1564234	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1571894	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061800	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404295	0.84[CHD][hapmap];0.87[JPT][hapmap]
rs2404302	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2404305	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404456	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3802454	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3802456	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3858089	0.85[ASN][1000 genomes]
rs4537362	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743979	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743980	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743981	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743982	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743984	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744422	0.90[CEU][hapmap];0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744423	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744424	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744425	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744426	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744428	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4744430	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744431	0.91[CEU][hapmap];0.93[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744432	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744433	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744435	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs4744436	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs6479588	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479591	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479592	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7020709	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021351	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022452	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048786	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048941	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851173	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7854831	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7857679	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7862156	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7863291	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865144	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871218	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7873479	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7873567	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs962229	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1571895	OGN	cis	parietal	SCAN
rs1571895	FOXE1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
4	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
5	chr9:97779400-97789200	Genic enhancers	Liver	Liver
6	chr9:97780600-97790800	Weak transcription	Fetal Brain Female	brain
7	chr9:97781200-97793600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:97781400-97793200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:97781400-97793600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:97782000-97792800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:97782600-97793600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:97783200-97789400	Enhancers	Brain Substantia Nigra	brain
13	chr9:97783400-97789000	Transcr. at gene 5' and 3'	A549	lung
14	chr9:97783600-97794000	Weak transcription	GM12878-XiMat	blood
15	chr9:97783800-97789000	Genic enhancers	HSMMtube	muscle
16	chr9:97783800-97789600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:97784200-97789200	Enhancers	Brain Hippocampus Middle	brain
18	chr9:97784400-97789000	Genic enhancers	NHEK	skin
19	chr9:97784600-97789000	Enhancers	Brain Cingulate Gyrus	brain
20	chr9:97785000-97789000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr9:97785000-97789200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:97785000-97789200	Enhancers	Fetal Kidney	kidney
23	chr9:97785200-97789000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:97785200-97789000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:97785200-97789000	Enhancers	Brain Anterior Caudate	brain
26	chr9:97785200-97789000	Genic enhancers	Fetal Intestine Small	intestine
27	chr9:97785400-97789000	Genic enhancers	Fetal Intestine Large	intestine
28	chr9:97785800-97789000	Enhancers	Stomach Mucosa	stomach
29	chr9:97786200-97790600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:97786200-97791800	Enhancers	Right Ventricle	heart
31	chr9:97786400-97790200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr9:97787000-97789000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:97787000-97789200	Genic enhancers	HSMM	muscle
34	chr9:97787000-97790200	Weak transcription	HMEC	breast
35	chr9:97787000-97794000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:97787400-97789200	Genic enhancers	NH-A	brain
37	chr9:97787600-97793000	Genic enhancers	HepG2	liver
38	chr9:97787800-97789000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:97787800-97789200	Enhancers	Rectal Smooth Muscle	rectum
40	chr9:97787800-97789200	Genic enhancers	NHDF-Ad	bronchial
41	chr9:97787800-97789200	Genic enhancers	NHLF	lung
42	chr9:97787800-97790200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97787800-97790200	Weak transcription	Gastric	stomach
44	chr9:97787800-97792800	Weak transcription	Spleen	Spleen
45	chr9:97787800-97793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:97787800-97795800	Genic enhancers	Osteobl	bone
47	chr9:97788000-97789000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:97788000-97790200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:97788000-97790200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:97788000-97791200	Weak transcription	Colonic Mucosa	Colon

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