Variant report

Variant	rs334348
Chromosome Location	chr9:101912471-101912472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101907167..101909352-chr9:101910696..101913205,3	K562	blood:
2	chr9:101910109..101913329-chr9:101915349..101919610,4	K562	blood:
3	chr9:101911700..101915310-chr9:101917488..101920239,4	K562	blood:
4	chr9:101906889..101909084-chr9:101911405..101913205,2	K562	blood:

Variant related genes	Relation type
ENSG00000252942	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1013186	0.89[CEU][hapmap]
rs10283455	0.89[CEU][hapmap]
rs10448292	0.81[EUR][1000 genomes]
rs10733708	0.96[ASN][1000 genomes]
rs10733709	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10739778	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs10739779	0.89[CEU][hapmap]
rs10760667	0.83[ASN][1000 genomes]
rs10760668	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10760669	0.85[ASN][1000 genomes]
rs10760670	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10760671	0.89[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10760672	0.89[CEU][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10760673	0.89[CEU][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10760674	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10819635	0.88[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs10819636	0.81[ASN][1000 genomes]
rs10819638	0.89[CEU][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10819639	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10819640	0.80[ASN][1000 genomes]
rs10988706	0.89[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10988709	0.81[ASN][1000 genomes]
rs10988713	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs10988715	0.81[ASN][1000 genomes]
rs10988716	0.89[CEU][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10988717	0.80[ASN][1000 genomes]
rs10988723	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11568752	0.81[ASN][1000 genomes]
rs12345675	0.87[EUR][1000 genomes]
rs12346650	0.88[ASW][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs12685571	0.81[ASN][1000 genomes]
rs12686783	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1571589	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1571590	0.89[CEU][hapmap]
rs1590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626340	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1699413	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1888223	0.83[ASN][1000 genomes]
rs1888225	0.82[ASN][1000 genomes]
rs1973518	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2026811	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs334349	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334351	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334353	0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334354	0.89[CEU][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs334355	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs334356	0.89[CEU][hapmap]
rs334357	0.89[CEU][hapmap]
rs334358	0.89[CEU][hapmap]
rs334362	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs334363	0.82[ASN][1000 genomes]
rs334364	0.82[ASN][1000 genomes]
rs334365	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334366	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334367	0.82[ASN][1000 genomes]
rs334368	0.85[EUR][1000 genomes]
rs334369	0.85[EUR][1000 genomes]
rs334371	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs367568	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3739798	0.82[ASN][1000 genomes]
rs383496	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs401186	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs420549	0.89[CEU][hapmap]
rs478061	0.85[EUR][1000 genomes]
rs597457	0.89[CEU][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6478972	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6478973	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7022989	0.85[CHB][hapmap]
rs7031302	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7031309	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7042852	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7043624	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7874221	0.89[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs868	0.89[CEU][hapmap]

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	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs334348	TGFBR1	cis	cerebellum	SCAN
rs334348	ZNF782	cis	cerebellum	SCAN
rs334348	LOC286359	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101890000-101914200	Weak transcription	Pancreas	Pancrea
2	chr9:101892600-101914200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:101892800-101921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:101895000-101914200	Weak transcription	Esophagus	oesophagus
5	chr9:101897600-101913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:101897600-101915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:101898000-101919400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:101899000-101913000	Strong transcription	HSMM	muscle
9	chr9:101899400-101913000	Weak transcription	Thymus	Thymus
10	chr9:101900200-101914800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr9:101900200-101915200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:101900800-101916800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr9:101902800-101914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:101902800-101915400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr9:101903000-101915200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr9:101903000-101921800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:101903200-101912600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:101903200-101913200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr9:101903200-101915000	Strong transcription	Osteobl	bone
20	chr9:101903400-101914200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:101903400-101915400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:101903600-101915000	Strong transcription	HSMMtube	muscle
23	chr9:101903600-101915200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:101903800-101913000	Strong transcription	Adipose Nuclei	Adipose
25	chr9:101904000-101913400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:101904000-101915800	Strong transcription	Placenta	Placenta
27	chr9:101904000-101916400	Strong transcription	Primary B cells from cord blood	blood
28	chr9:101904000-101917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:101904200-101913200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:101904200-101914800	Strong transcription	Liver	Liver
31	chr9:101904600-101916200	Weak transcription	Fetal Intestine Small	intestine
32	chr9:101905400-101912600	Strong transcription	NH-A	brain
33	chr9:101905800-101913000	Strong transcription	NHDF-Ad	bronchial
34	chr9:101906200-101915000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:101906200-101915000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:101906400-101913000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:101906800-101913400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:101907000-101913200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr9:101907200-101919800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:101907800-101916600	Weak transcription	Fetal Brain Male	brain
41	chr9:101908000-101914400	Weak transcription	Small Intestine	intestine
42	chr9:101908200-101922000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:101908400-101914200	Weak transcription	Brain Substantia Nigra	brain
44	chr9:101908400-101916600	Weak transcription	NHLF	lung
45	chr9:101908400-101918000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:101908600-101914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:101908600-101914200	Weak transcription	Aorta	Aorta
48	chr9:101908600-101924600	Weak transcription	Gastric	stomach
49	chr9:101909000-101918600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:101909000-101920000	Weak transcription	HepG2	liver

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