Variant report

Variant	rs601746
Chromosome Location	chr10:96942283-96942284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96941976..96944883-chr10:96989765..96992078,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234026	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10509681	1.00[ASN][1000 genomes]
rs11188124	1.00[ASN][1000 genomes]
rs11188148	1.00[ASN][1000 genomes]
rs11188153	1.00[ASN][1000 genomes]
rs11188154	1.00[ASN][1000 genomes]
rs11572064	1.00[ASN][1000 genomes]
rs11572080	1.00[ASN][1000 genomes]
rs11572082	1.00[ASN][1000 genomes]
rs11572094	1.00[ASN][1000 genomes]
rs11572100	0.80[YRI][hapmap]
rs11572107	1.00[ASN][1000 genomes]
rs11572116	1.00[ASN][1000 genomes]
rs11572128	1.00[ASN][1000 genomes]
rs11572150	1.00[ASN][1000 genomes]
rs11572168	1.00[ASN][1000 genomes]
rs11572169	1.00[ASN][1000 genomes]
rs11572170	0.80[YRI][hapmap]
rs11572174	1.00[ASN][1000 genomes]
rs11591385	1.00[ASN][1000 genomes]
rs11593816	1.00[ASN][1000 genomes]
rs11598823	1.00[ASN][1000 genomes]
rs11599166	1.00[CHD][hapmap]
rs12761249	1.00[ASN][1000 genomes]
rs12761315	1.00[ASN][1000 genomes]
rs12762602	1.00[ASN][1000 genomes]
rs12762652	1.00[ASN][1000 genomes]
rs12763201	1.00[ASN][1000 genomes]
rs12763939	1.00[ASN][1000 genomes]
rs12766965	1.00[ASN][1000 genomes]
rs12774244	1.00[ASN][1000 genomes]
rs12777852	1.00[ASN][1000 genomes]
rs12778481	1.00[ASN][1000 genomes]
rs12779007	1.00[ASN][1000 genomes]
rs12779339	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780333	1.00[ASN][1000 genomes]
rs12784371	1.00[ASN][1000 genomes]
rs1620060	1.00[YRI][hapmap]
rs17452671	1.00[ASN][1000 genomes]
rs17452714	1.00[ASN][1000 genomes]
rs17453533	1.00[ASN][1000 genomes]
rs17523627	1.00[ASN][1000 genomes]
rs17524348	1.00[ASN][1000 genomes]
rs17525659	1.00[ASN][1000 genomes]
rs1934954	1.00[ASN][1000 genomes]
rs2153629	1.00[ASN][1000 genomes]
rs2185570	1.00[ASN][1000 genomes]
rs2901832	0.84[MEX][hapmap]
rs34031095	1.00[ASN][1000 genomes]
rs34119978	1.00[ASN][1000 genomes]
rs34246390	1.00[ASN][1000 genomes]
rs34254643	1.00[ASN][1000 genomes]
rs34320910	1.00[ASN][1000 genomes]
rs34409900	1.00[ASN][1000 genomes]
rs34462937	1.00[ASN][1000 genomes]
rs34729632	1.00[ASN][1000 genomes]
rs34883883	1.00[ASN][1000 genomes]
rs34949438	1.00[ASN][1000 genomes]
rs35203700	1.00[ASN][1000 genomes]
rs35213500	1.00[ASN][1000 genomes]
rs35238981	1.00[ASN][1000 genomes]
rs35432490	1.00[ASN][1000 genomes]
rs35461306	1.00[ASN][1000 genomes]
rs35598837	1.00[ASN][1000 genomes]
rs35883122	1.00[ASN][1000 genomes]
rs35955220	1.00[ASN][1000 genomes]
rs35998772	1.00[ASN][1000 genomes]
rs36037322	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36042065	1.00[ASN][1000 genomes]
rs36168663	1.00[ASN][1000 genomes]
rs45457395	1.00[ASN][1000 genomes]
rs45523137	1.00[ASN][1000 genomes]
rs45535939	1.00[ASN][1000 genomes]
rs45546031	1.00[ASN][1000 genomes]
rs45601238	1.00[ASN][1000 genomes]
rs4607998	1.00[ASN][1000 genomes]
rs483239	1.00[ASN][1000 genomes]
rs485102	0.80[YRI][hapmap]
rs4918795	1.00[ASN][1000 genomes]
rs507728	1.00[ASN][1000 genomes]
rs55753924	1.00[ASN][1000 genomes]
rs56028148	1.00[ASN][1000 genomes]
rs56408997	1.00[ASN][1000 genomes]
rs570849	1.00[ASN][1000 genomes]
rs584227	0.89[AFR][1000 genomes]
rs595924	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs616450	0.86[AFR][1000 genomes]
rs61886802	1.00[ASN][1000 genomes]
rs623544	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs626465	1.00[CHD][hapmap];1.00[YRI][hapmap]
rs634782	0.89[AFR][1000 genomes]
rs639937	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs650243	1.00[CHD][hapmap];0.80[YRI][hapmap]
rs659309	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66648066	1.00[ASN][1000 genomes]
rs66816038	1.00[ASN][1000 genomes]
rs670565	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67403627	1.00[ASN][1000 genomes]
rs67728892	1.00[ASN][1000 genomes]
rs67737822	1.00[ASN][1000 genomes]
rs67851687	1.00[ASN][1000 genomes]
rs67918795	1.00[ASN][1000 genomes]
rs680829	1.00[CHD][hapmap];0.96[LWK][hapmap];0.86[MKK][hapmap];0.80[YRI][hapmap]
rs682349	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs684203	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs686705	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs701889	1.00[ASN][1000 genomes]
rs7082506	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099702	1.00[ASN][1000 genomes]
rs71482344	1.00[ASN][1000 genomes]
rs71505737	1.00[ASN][1000 genomes]
rs72818651	1.00[ASN][1000 genomes]
rs72818652	1.00[ASN][1000 genomes]
rs72818673	1.00[ASN][1000 genomes]
rs72818680	1.00[ASN][1000 genomes]
rs72818681	1.00[ASN][1000 genomes]
rs72820645	1.00[ASN][1000 genomes]
rs7916421	1.00[CHD][hapmap]
rs815241	1.00[YRI][hapmap]
rs9332216	1.00[ASN][1000 genomes]
rs9332222	1.00[ASN][1000 genomes]
rs9332242	1.00[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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1834151	chr10:96925446-96992955	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs601746	PI4K2A	cis	cerebellum	SCAN
rs601746	CYP2C18	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96932000-96943000	Weak transcription	Pancreas	Pancrea
2	chr10:96936800-96942400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:96941400-96942400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr10:96941400-96942800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr10:96941400-96942800	Enhancers	Fetal Intestine Small	intestine
6	chr10:96941400-96942800	Enhancers	HUVEC	blood vessel
7	chr10:96941600-96942400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:96941600-96942600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr10:96941600-96942800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr10:96941600-96942800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:96941600-96943000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:96941800-96942400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:96941800-96942600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:96941800-96942800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:96941800-96943000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:96942000-96942800	Weak transcription	A549	lung
17	chr10:96942000-96942800	Weak transcription	NHDF-Ad	bronchial
18	chr10:96942000-96943000	Weak transcription	Stomach Mucosa	stomach
19	chr10:96942000-96943800	Weak transcription	Fetal Lung	lung
20	chr10:96942000-96948200	Weak transcription	HepG2	liver
21	chr10:96942200-96942400	Enhancers	Fetal Intestine Large	intestine
22	chr10:96942200-96942600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr10:96942200-96942600	Flanking Active TSS	Liver	Liver
24	chr10:96942200-96942800	Enhancers	Fetal Kidney	kidney

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