Variant report

Variant	rs6479591
Chromosome Location	chr9:97795421-97795422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97786821..97789606-chr9:97794967..97796572,3	K562	blood:
2	chr9:97794089..97795756-chr9:97801437..97804399,2	K562	blood:
3	chr9:97795205..97797752-chr9:97832008..97833533,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIATL1-7	chr9:97794314-97795781	ENSG00000251631
2	lnc-FANCC-3	chr9:97794312-97795781	NONHSAT133343

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1004373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10117370	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10121760	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512253	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.91[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10761366	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761368	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761369	0.83[CEU][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs10761372	0.84[AFR][1000 genomes]
rs10993427	0.88[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993456	0.82[TSI][hapmap]
rs10993464	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993467	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12339639	0.82[TSI][hapmap]
rs1412488	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1564234	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1571894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1571895	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]
rs2061800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404295	0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs2404302	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap]
rs2404305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802456	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3858089	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4537362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743980	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743981	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743982	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744422	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744423	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744428	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4744430	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744431	0.91[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744432	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744436	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes]
rs6479588	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479592	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]
rs7020709	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7022452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043705	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7048786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7851173	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7854831	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7857679	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7862156	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7865144	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7871218	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7873479	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7873567	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs962229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479591	OGN	cis	parietal	SCAN
rs6479591	FOXE1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97787800-97795800	Genic enhancers	Osteobl	bone
3	chr9:97788400-97795800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:97788800-97795800	Enhancers	Psoas Muscle	Psoas
5	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:97790000-97795800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:97790000-97796800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:97790200-97795600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:97790200-97795800	Enhancers	Right Atrium	heart
10	chr9:97790200-97796000	Enhancers	Brain Angular Gyrus	brain
11	chr9:97790200-97796400	Genic enhancers	HSMM	muscle
12	chr9:97790600-97795800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:97790800-97795600	Genic enhancers	Fetal Intestine Small	intestine
14	chr9:97791200-97795600	Genic enhancers	Liver	Liver
15	chr9:97791200-97795800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:97791400-97795800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:97791600-97799600	Weak transcription	Hela-S3	cervix
18	chr9:97791600-97800000	Weak transcription	Placenta	Placenta
19	chr9:97792600-97795800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr9:97792800-97795600	Genic enhancers	Fetal Stomach	stomach
21	chr9:97792800-97795600	Enhancers	Right Ventricle	heart
22	chr9:97792800-97795800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr9:97792800-97795800	Enhancers	Stomach Mucosa	stomach
24	chr9:97793000-97795800	Enhancers	Brain Cingulate Gyrus	brain
25	chr9:97793000-97795800	Enhancers	Pancreas	Pancrea
26	chr9:97793000-97796000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:97793000-97797200	Enhancers	Brain Substantia Nigra	brain
28	chr9:97793000-97800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:97793200-97795800	Genic enhancers	HSMMtube	muscle
30	chr9:97793200-97796000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:97793200-97802200	Weak transcription	Fetal Kidney	kidney
32	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
33	chr9:97793600-97795600	Enhancers	Primary hematopoietic stem cells	blood
34	chr9:97793600-97795600	Enhancers	Fetal Intestine Large	intestine
35	chr9:97793600-97798200	Weak transcription	NHDF-Ad	bronchial
36	chr9:97793800-97795600	Enhancers	Duodenum Mucosa	Duodenum
37	chr9:97793800-97795600	Enhancers	Lung	lung
38	chr9:97793800-97795600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr9:97793800-97795800	Enhancers	Brain Anterior Caudate	brain
40	chr9:97793800-97795800	Enhancers	Esophagus	oesophagus
41	chr9:97793800-97795800	Enhancers	Small Intestine	intestine
42	chr9:97793800-97800000	Weak transcription	Adipose Nuclei	Adipose
43	chr9:97794000-97795600	Enhancers	Spleen	Spleen
44	chr9:97794000-97796800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:97794000-97799800	Weak transcription	Fetal Lung	lung
46	chr9:97794200-97795600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:97794200-97795600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
48	chr9:97794200-97805800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:97794400-97795600	Enhancers	K562	blood

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