Variant report

Variant	rs7452626
Chromosome Location	chr6:36640241-36640242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1321312	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1969701	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1977172	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3176330	0.96[ASN][1000 genomes]
rs3176331	0.89[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3829966	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829967	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829968	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135234	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4135237	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4135239	0.97[ASN][1000 genomes]
rs4713997	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457936	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902994	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6907801	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926780	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762623	0.89[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs9380585	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380586	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv602946	chr6:36633160-36641478	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv602947	chr6:36637597-36641157	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv13626	chr6:36640176-36642182	Enhancers Weak transcription	CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7452626	ITPR3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:36635200-36643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:36635400-36644000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
5	chr6:36635600-36644000	Weak transcription	Hela-S3	cervix
6	chr6:36636000-36640800	Enhancers	Fetal Intestine Small	intestine
7	chr6:36636400-36643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:36636400-36643800	Weak transcription	NH-A	brain
9	chr6:36636800-36641000	Enhancers	Fetal Intestine Large	intestine
10	chr6:36637000-36643800	Weak transcription	Osteobl	bone
11	chr6:36637200-36641600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:36637200-36641600	Weak transcription	GM12878-XiMat	blood
13	chr6:36637200-36643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:36637200-36643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:36637200-36643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:36637200-36643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:36637200-36643800	Weak transcription	HSMM	muscle
18	chr6:36637400-36642600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:36637800-36642600	Weak transcription	HSMMtube	muscle
20	chr6:36637800-36643400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:36637800-36643400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:36637800-36643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:36637800-36643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:36638800-36644200	Weak transcription	Ovary	ovary
25	chr6:36639600-36640400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr6:36640000-36643800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:36640000-36643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:36640000-36644000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:36640200-36641600	Weak transcription	Placenta	Placenta
30	chr6:36640200-36642000	Weak transcription	HepG2	liver
31	chr6:36640200-36642400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:36640200-36643800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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