Variant report

Variant	rs7021351
Chromosome Location	chr9:97793139-97793140
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97791289..97793582-chr9:97853696..97856435,2	MCF-7	breast:
2	chr9:97785869..97788341-chr9:97791572..97794035,3	MCF-7	breast:
3	chr9:97793038..97795418-chr9:97797884..97800566,2	K562	blood:
4	chr9:97683038..97684583-chr9:97793134..97794968,2	MCF-7	breast:
5	chr9:97443362..97445531-chr9:97792308..97793975,2	MCF-7	breast:
6	chr9:97792342..97793987-chr9:97802659..97804912,2	K562	blood:
7	chr9:97792211..97795140-chr9:97806961..97811123,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIATL1-7	chr9:97792029-97794143	ENSG00000251631
2	lnc-FANCC-3	chr9:97792029-97794141	NONHSAT133343

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1004373	1.00[CEU][hapmap];1.00[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];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[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];0.82[CHB][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];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10512253	0.91[CEU][hapmap];1.00[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];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.89[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];0.82[CHB][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];0.94[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	0.88[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];0.82[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1564234	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1571894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571895	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]
rs2061800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404295	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs2404302	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2404305	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]
rs2404456	1.00[CEU][hapmap];1.00[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];0.88[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];0.88[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];1.00[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];1.00[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];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[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];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744423	0.91[CEU][hapmap];0.88[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];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]
rs4744425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744426	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];0.84[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];1.00[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];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744432	0.91[CEU][hapmap];1.00[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];1.00[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];0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs4744436	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs6479588	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479591	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]
rs6479592	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]
rs7020709	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7022452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[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];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[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];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[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];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7863291	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];0.86[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	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]

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
rs7021351	OGN	cis	parietal	SCAN
rs7021351	FOXE1	cis	parietal	SCAN

Chromatin state (count:91 , 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	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
3	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
4	chr9:97781200-97793600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:97781400-97793200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:97781400-97793600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:97782600-97793600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:97783600-97794000	Weak transcription	GM12878-XiMat	blood
9	chr9:97787000-97794000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:97787800-97793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:97787800-97795800	Genic enhancers	Osteobl	bone
12	chr9:97788000-97794800	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr9:97788200-97794400	Weak transcription	K562	blood
14	chr9:97788400-97795800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr9:97788800-97795000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:97788800-97795800	Enhancers	Psoas Muscle	Psoas
17	chr9:97789000-97794200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:97789000-97794400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:97790000-97794400	Genic enhancers	NH-A	brain
21	chr9:97790000-97795800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:97790000-97796800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:97790200-97793400	Enhancers	Brain Anterior Caudate	brain
24	chr9:97790200-97794600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:97790200-97794600	Genic enhancers	Left Ventricle	heart
26	chr9:97790200-97795600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:97790200-97795800	Enhancers	Right Atrium	heart
28	chr9:97790200-97796000	Enhancers	Brain Angular Gyrus	brain
29	chr9:97790200-97796400	Genic enhancers	HSMM	muscle
30	chr9:97790600-97793200	Enhancers	Fetal Muscle Leg	muscle
31	chr9:97790600-97793600	Genic enhancers	Fetal Intestine Large	intestine
32	chr9:97790600-97794000	Enhancers	Brain Hippocampus Middle	brain
33	chr9:97790600-97794800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:97790600-97795800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:97790800-97795600	Genic enhancers	Fetal Intestine Small	intestine
36	chr9:97791000-97794000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:97791000-97794000	Weak transcription	HMEC	breast
38	chr9:97791200-97795600	Genic enhancers	Liver	Liver
39	chr9:97791200-97795800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:97791400-97795800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:97791600-97793800	Weak transcription	Colonic Mucosa	Colon
42	chr9:97791600-97799600	Weak transcription	Hela-S3	cervix
43	chr9:97791600-97800000	Weak transcription	Placenta	Placenta
44	chr9:97791800-97793800	Weak transcription	Lung	lung
45	chr9:97791800-97793800	Weak transcription	Small Intestine	intestine
46	chr9:97791800-97794000	Enhancers	Colon Smooth Muscle	Colon
47	chr9:97791800-97794000	Weak transcription	Gastric	stomach
48	chr9:97791800-97795400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr9:97792000-97793200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:97792000-97793800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links