Variant report

Variant	rs9530958
Chromosome Location	chr13:80354887-80354888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10507900	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11619959	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12019641	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12428029	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12867107	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1335288	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1414110	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2039554	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2039555	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2039556	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2152226	0.84[EUR][1000 genomes]
rs2248409	0.84[EUR][1000 genomes]
rs2248413	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2248563	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2262460	0.91[EUR][1000 genomes]
rs2329137	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329138	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783085	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2802634	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2802638	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2802640	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2802641	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35661635	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4885658	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4885660	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4885669	0.85[EUR][1000 genomes]
rs7322877	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7327527	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7984156	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs915260	0.90[EUR][1000 genomes]
rs9530959	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9545191	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9545203	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9545205	0.86[EUR][1000 genomes];0.88[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	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv900590	chr13:80342186-80421340	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9530958	HIST1H2AM	trans	cerebellum	SCAN
rs9530958	HES2	trans	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80349600-80357600	Enhancers	Fetal Intestine Large	intestine
2	chr13:80349800-80358600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:80350800-80356000	Weak transcription	Fetal Lung	lung
4	chr13:80351000-80356000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:80351000-80356000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:80351000-80356200	Weak transcription	HUVEC	blood vessel
7	chr13:80351800-80356200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:80351800-80356200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr13:80353200-80355000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:80353200-80358800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr13:80353400-80355000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:80353400-80355000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:80353600-80355000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:80353600-80355000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:80353600-80355400	Enhancers	HSMMtube	muscle
16	chr13:80353800-80355000	Enhancers	Fetal Muscle Leg	muscle
17	chr13:80353800-80355000	Flanking Active TSS	Osteobl	bone
18	chr13:80353800-80355400	Enhancers	NH-A	brain
19	chr13:80354000-80355000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:80354000-80355000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:80354000-80355200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:80354000-80356200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr13:80354000-80356800	Weak transcription	Stomach Mucosa	stomach
24	chr13:80354000-80357000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr13:80354200-80355000	Enhancers	Fetal Thymus	thymus
26	chr13:80354200-80356400	Weak transcription	Brain Substantia Nigra	brain
27	chr13:80354200-80356800	Weak transcription	Small Intestine	intestine
28	chr13:80354400-80355800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr13:80354400-80355800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr13:80354400-80355800	Weak transcription	Fetal Heart	heart
31	chr13:80354400-80356200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:80354400-80356400	Weak transcription	Fetal Intestine Small	intestine
33	chr13:80354400-80356800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr13:80354600-80355000	Enhancers	Spleen	Spleen
35	chr13:80354600-80355000	Enhancers	HSMM	muscle
36	chr13:80354600-80355000	Flanking Active TSS	NHLF	lung
37	chr13:80354600-80355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:80354600-80356000	Weak transcription	Fetal Kidney	kidney
39	chr13:80354600-80356000	Weak transcription	Hela-S3	cervix
40	chr13:80354600-80356200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr13:80354600-80356200	Weak transcription	A549	lung
42	chr13:80354600-80356400	Weak transcription	Brain Anterior Caudate	brain
43	chr13:80354600-80356400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr13:80354600-80357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:80354800-80355000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:80354800-80355000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:80354800-80355000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:80354800-80355200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr13:80354800-80355400	Enhancers	HMEC	breast
50	chr13:80354800-80355400	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links