Variant report

Variant	rs962229
Chromosome Location	chr9:97792167-97792168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr9:97790920..97793019-chr9:97799346..97801505,2	K562	blood:

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

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1004373	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[CHB][hapmap];1.00[JPT][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	0.82[CHB][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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761364	0.88[CHB][hapmap];0.87[JPT][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	0.82[CHB][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	0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs10993427	0.89[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
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]
rs1412488	0.82[CHB][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	0.89[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[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571895	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]
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[JPT][hapmap]
rs2404302	0.89[CHB][hapmap]
rs2404305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3802454	0.89[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3802456	0.89[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[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743979	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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744422	0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744423	0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744424	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[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[CHB][hapmap];1.00[JPT][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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744431	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744435	0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs4744436	0.83[JPT][hapmap]
rs6479588	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[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7020709	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021351	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]
rs7022452	1.00[CHB][hapmap];1.00[JPT][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[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851173	0.88[CHB][hapmap];0.87[JPT][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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7863291	1.00[CHB][hapmap];1.00[JPT][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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs962229	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

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	chr9:97782000-97792800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:97782600-97793600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:97783600-97794000	Weak transcription	GM12878-XiMat	blood
10	chr9:97787000-97794000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:97787600-97793000	Genic enhancers	HepG2	liver
12	chr9:97787800-97792800	Weak transcription	Spleen	Spleen
13	chr9:97787800-97793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:97787800-97795800	Genic enhancers	Osteobl	bone
15	chr9:97788000-97794800	Genic enhancers	Muscle Satellite Cultured Cells	--
16	chr9:97788200-97792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:97788200-97793000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:97788200-97794400	Weak transcription	K562	blood
19	chr9:97788400-97795800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:97788800-97792200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr9:97788800-97792800	Weak transcription	Adipose Nuclei	Adipose
22	chr9:97788800-97795000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:97788800-97795800	Enhancers	Psoas Muscle	Psoas
24	chr9:97789000-97793000	Weak transcription	Aorta	Aorta
25	chr9:97789000-97793000	Weak transcription	HUVEC	blood vessel
26	chr9:97789000-97794200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:97789000-97794400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:97789800-97792400	Enhancers	Fetal Lung	lung
30	chr9:97789800-97792800	Enhancers	Brain Substantia Nigra	brain
31	chr9:97789800-97792800	Enhancers	Fetal Heart	heart
32	chr9:97790000-97792200	Transcr. at gene 5' and 3'	A549	lung
33	chr9:97790000-97794400	Genic enhancers	NH-A	brain
34	chr9:97790000-97795800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:97790000-97796800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:97790200-97792200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr9:97790200-97792800	Enhancers	Pancreas	Pancrea
38	chr9:97790200-97792800	Genic enhancers	HSMMtube	muscle
39	chr9:97790200-97793400	Enhancers	Brain Anterior Caudate	brain
40	chr9:97790200-97794600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:97790200-97794600	Genic enhancers	Left Ventricle	heart
42	chr9:97790200-97795600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97790200-97795800	Enhancers	Right Atrium	heart
44	chr9:97790200-97796000	Enhancers	Brain Angular Gyrus	brain
45	chr9:97790200-97796400	Genic enhancers	HSMM	muscle
46	chr9:97790400-97792800	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:97790600-97792200	Enhancers	Ovary	ovary
48	chr9:97790600-97793000	Genic enhancers	NHDF-Ad	bronchial
49	chr9:97790600-97793200	Enhancers	Fetal Muscle Leg	muscle
50	chr9:97790600-97793600	Genic enhancers	Fetal Intestine Large	intestine

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