Variant report

Variant	rs9497426
Chromosome Location	chr6:146234644-146234645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146230814..146232916-chr6:146233630..146237382,3	K562	blood:
2	chr6:146233246..146236996-chr6:146247458..146250759,3	K562	blood:
3	chr6:146234113..146237029-chr6:146245031..146246737,2	K562	blood:

Variant related genes	Relation type
ENSG00000146414	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1011597	0.84[JPT][hapmap]
rs10872580	0.84[JPT][hapmap]
rs12199362	0.84[JPT][hapmap]
rs1337841	0.84[JPT][hapmap]
rs1415746	0.84[JPT][hapmap]
rs1415747	0.84[JPT][hapmap]
rs1890171	0.84[JPT][hapmap]
rs2050027	0.84[JPT][hapmap]
rs2064185	0.83[JPT][hapmap]
rs2142980	0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2235481	0.83[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs2253757	0.83[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2265470	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2485631	0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs34541797	0.84[ASN][1000 genomes]
rs3811102	0.84[JPT][hapmap]
rs4895683	0.84[JPT][hapmap]
rs6570732	0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6900175	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs6906258	0.84[JPT][hapmap]
rs6906402	0.84[JPT][hapmap]
rs6912351	0.81[ASN][1000 genomes]
rs6915718	0.84[JPT][hapmap]
rs7746618	0.80[ASN][1000 genomes]
rs7752286	0.84[JPT][hapmap]
rs7753273	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7753770	0.84[JPT][hapmap]
rs9285508	0.92[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9373475	0.83[JPT][hapmap]
rs9376961	0.84[JPT][hapmap]
rs9386136	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs9390353	0.83[JPT][hapmap]
rs9390356	0.84[JPT][hapmap]
rs9497403	0.83[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][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	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9497426	SHPRH	cis	cerebellum	SCAN
rs9497426	SHPRH	cis	parietal	SCAN
rs9497426	EPM2A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146207800-146240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:146210400-146282000	Weak transcription	Spleen	Spleen
3	chr6:146211600-146236000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:146215000-146242200	Weak transcription	Hela-S3	cervix
5	chr6:146219200-146249200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:146219200-146276600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:146219600-146250600	Strong transcription	Dnd41	blood
8	chr6:146219800-146271400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:146220000-146249400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:146220000-146255200	Weak transcription	Gastric	stomach
11	chr6:146220000-146259400	Weak transcription	Esophagus	oesophagus
12	chr6:146220000-146276800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:146220000-146283200	Weak transcription	Small Intestine	intestine
14	chr6:146220200-146268400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:146220400-146255200	Weak transcription	Fetal Intestine Small	intestine
16	chr6:146223800-146248600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:146224600-146257000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:146224800-146235800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:146224800-146235800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:146224800-146235800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:146224800-146237200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr6:146225200-146268600	Weak transcription	Stomach Mucosa	stomach
23	chr6:146225400-146235000	Strong transcription	Brain Germinal Matrix	brain
24	chr6:146225400-146248400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:146225400-146249600	Strong transcription	Adipose Nuclei	Adipose
26	chr6:146225600-146235800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:146225600-146237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:146225800-146235600	Strong transcription	Placenta	Placenta
29	chr6:146225800-146243800	Weak transcription	Psoas Muscle	Psoas
30	chr6:146226000-146249000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:146226000-146249600	Strong transcription	Liver	Liver
32	chr6:146226200-146284200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:146226400-146236200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:146226400-146268600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:146226600-146236200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:146226600-146249200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:146226800-146235600	Strong transcription	Fetal Brain Female	brain
38	chr6:146226800-146249400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:146226800-146270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:146227000-146235800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:146227200-146236000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:146227200-146248400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr6:146227200-146268800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:146227400-146236200	Strong transcription	Fetal Kidney	kidney
45	chr6:146227400-146241200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr6:146227400-146248400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:146227600-146248400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:146227800-146234800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr6:146227800-146235800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr6:146227800-146248200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links