Variant report

Variant	rs12235970
Chromosome Location	chr9:97050164-97050165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10435925	0.83[AMR][1000 genomes]
rs10435926	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10993127	0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10993130	0.80[ASN][1000 genomes]
rs10993131	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10993137	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10993139	0.92[AMR][1000 genomes]
rs10993140	0.90[ASN][1000 genomes]
rs10993143	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993144	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993147	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993151	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11533012	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11535539	0.89[AMR][1000 genomes]
rs12235386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236219	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12347577	0.80[ASN][1000 genomes]
rs1328305	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16909983	0.83[CHB][hapmap];0.81[YRI][hapmap]
rs16910109	0.83[CHB][hapmap]
rs1752784	0.90[CHD][hapmap]
rs2486632	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs2769813	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs2769816	0.83[CHB][hapmap]
rs3118766	0.95[JPT][hapmap]
rs4744338	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs4744345	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs639276	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs7024151	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7024423	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7024915	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7027606	0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7028040	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7028530	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7042481	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs7045405	0.87[ASN][1000 genomes]
rs7858082	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9409515	0.90[AMR][1000 genomes]
rs9409546	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs9695761	0.90[ASN][1000 genomes]
rs9696597	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv968732	chr9:97043511-97050792	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12235970	HIATL1	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
2	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
4	chr9:97023000-97055400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:97031800-97050400	Weak transcription	Psoas Muscle	Psoas
6	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:97033600-97054600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:97037400-97050200	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:97039200-97053600	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:97039200-97055000	Weak transcription	Brain Substantia Nigra	brain
12	chr9:97039200-97062600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:97039400-97054600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:97040000-97064600	Weak transcription	Brain Germinal Matrix	brain
16	chr9:97041200-97051600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:97041200-97054400	Weak transcription	NHDF-Ad	bronchial
18	chr9:97041200-97054600	Weak transcription	Stomach Mucosa	stomach
19	chr9:97041200-97065400	Weak transcription	Small Intestine	intestine
20	chr9:97041400-97053600	Weak transcription	HepG2	liver
21	chr9:97041800-97054800	Weak transcription	Fetal Brain Male	brain
22	chr9:97042200-97054400	Weak transcription	Spleen	Spleen
23	chr9:97042200-97055400	Weak transcription	Esophagus	oesophagus
24	chr9:97042400-97050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:97042400-97050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:97042600-97061400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:97042600-97068400	Weak transcription	Fetal Brain Female	brain
28	chr9:97042800-97050200	Weak transcription	HSMMtube	muscle
29	chr9:97042800-97050600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:97042800-97054600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:97042800-97054600	Weak transcription	Fetal Kidney	kidney
32	chr9:97042800-97057000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:97042800-97064000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr9:97042800-97064400	Weak transcription	Hela-S3	cervix
35	chr9:97043000-97050800	Weak transcription	NHEK	skin
36	chr9:97043000-97051200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:97043000-97053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:97043000-97053600	Weak transcription	Brain Anterior Caudate	brain
39	chr9:97043000-97054200	Weak transcription	Osteobl	bone
40	chr9:97043000-97057000	Weak transcription	HUVEC	blood vessel
41	chr9:97043000-97061400	Weak transcription	Fetal Thymus	thymus
42	chr9:97043200-97050200	Weak transcription	Fetal Muscle Leg	muscle
43	chr9:97043200-97050200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:97043200-97050400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:97043200-97050400	Weak transcription	Lung	lung
46	chr9:97043200-97051600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:97043200-97051600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:97043200-97053600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:97043200-97054800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:97043200-97054800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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