Variant report

Variant	rs7917640
Chromosome Location	chr10:90106708-90106709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89622149..89624843-chr10:90106661..90108440,2	MCF-7	breast:
2	chr10:89619839..89624557-chr10:90105061..90108196,4	MCF-7	breast:
3	chr10:90105977..90106882-chr10:90145125..90145815,2	MCF-7	breast:
4	chr10:90105325..90109071-chr10:90144209..90148400,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction
ENSG00000227268	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10749577	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788592	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10887800	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10887801	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10887802	0.81[ASN][1000 genomes]
rs10887803	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10887804	0.81[ASN][1000 genomes]
rs10887805	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10887806	0.87[ASN][1000 genomes]
rs10887818	0.82[JPT][hapmap]
rs11202712	0.86[ASN][1000 genomes]
rs11202713	0.86[ASN][1000 genomes]
rs11202715	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11202716	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11202723	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1342451	0.82[JPT][hapmap]
rs1346226	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1426618	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1426619	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1582784	0.82[ASN][1000 genomes]
rs1617881	0.85[JPT][hapmap]
rs2433340	0.86[JPT][hapmap]
rs4933476	0.86[ASN][1000 genomes]
rs4934403	0.82[JPT][hapmap]
rs61853517	0.81[ASN][1000 genomes]
rs6586125	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6586128	0.80[ASN][1000 genomes]
rs6586129	0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6586132	0.90[JPT][hapmap]
rs7069120	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7089911	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7091137	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7096330	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7895582	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7895674	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7899861	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7905573	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7905600	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7918921	0.81[JPT][hapmap]
rs7920126	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs792205	0.82[JPT][hapmap]
rs792209	0.82[JPT][hapmap]
rs792230	0.82[JPT][hapmap]
rs792234	0.87[JPT][hapmap]
rs796945	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs919115	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv551838	chr10:90058637-90137045	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7917640	IFIT1B	cis	cerebellum	SCAN
rs7917640	TIMM17A	trans	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90103800-90107200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr10:90104000-90107800	Weak transcription	Adipose Nuclei	Adipose
3	chr10:90104000-90108000	Weak transcription	Ovary	ovary
4	chr10:90104200-90107000	Weak transcription	HSMMtube	muscle
5	chr10:90104400-90109000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:90104600-90107200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr10:90104600-90108200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:90104800-90106800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr10:90104800-90108400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr10:90104800-90108800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr10:90104800-90108800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr10:90104800-90109200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr10:90105000-90107800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:90105600-90108200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr10:90105800-90107400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr10:90106000-90107000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr10:90106000-90107400	Enhancers	Liver	Liver
18	chr10:90106000-90107600	Enhancers	Fetal Heart	heart
19	chr10:90106000-90108200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr10:90106200-90108400	Weak transcription	Primary B cells from cord blood	blood
21	chr10:90106400-90107000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:90106400-90107000	Enhancers	Fetal Kidney	kidney
23	chr10:90106400-90107200	Enhancers	Fetal Lung	lung
24	chr10:90106400-90107400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr10:90106400-90108600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr10:90106400-90108800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr10:90106600-90106800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:90106600-90107000	Weak transcription	Colon Smooth Muscle	Colon
29	chr10:90106600-90107200	Enhancers	Right Atrium	heart
30	chr10:90106600-90107800	Weak transcription	Dnd41	blood
31	chr10:90106600-90108200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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