Variant report

Variant	rs7139630
Chromosome Location	chr13:53306304-53306305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53303661..53305233-chr13:53305750..53308464,2	K562	blood:
2	chr13:53305786..53308758-chr13:53309005..53310904,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1057478	0.85[CHB][hapmap]
rs11616261	0.81[ASN][1000 genomes]
rs2038826	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2147676	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2147692	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2575960	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs342768	0.86[ASN][1000 genomes]
rs342770	0.86[ASN][1000 genomes]
rs3742297	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4284531	0.85[CHB][hapmap]
rs4884235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs616969	0.82[ASN][1000 genomes]
rs6561671	0.88[ASN][1000 genomes]
rs6561675	0.88[ASN][1000 genomes]
rs7139495	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7324427	0.91[ASN][1000 genomes]
rs7328729	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7334137	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7334677	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs7336771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7337021	0.90[ASN][1000 genomes]
rs7399901	0.87[ASN][1000 genomes]
rs7999849	0.82[ASN][1000 genomes]
rs9526951	0.81[ASN][1000 genomes]
rs9526968	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9526974	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9526975	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9526982	0.83[ASN][1000 genomes]
rs9536197	0.88[ASN][1000 genomes]
rs9536211	0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9536217	0.82[ASN][1000 genomes]
rs9536219	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9536220	0.83[CHB][hapmap]
rs9536223	0.81[ASN][1000 genomes]
rs9536236	0.83[ASN][1000 genomes]
rs9536247	0.85[ASN][1000 genomes]
rs9536262	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9563113	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9563114	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9568750	0.89[ASN][1000 genomes]
rs9568751	0.90[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	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7139630	CAB39L	cis	parietal	SCAN
rs7139630	HNRNPA1L2	cis	cerebellum	SCAN
rs7139630	CKAP2	cis	cerebellum	SCAN
rs7139630	SUGT1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53286800-53310800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:53298400-53310600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:53299000-53310400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:53303400-53308600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr13:53303800-53311400	Weak transcription	Brain Anterior Caudate	brain
6	chr13:53304800-53306400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:53304800-53308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr13:53304800-53308600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr13:53304800-53308600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr13:53304800-53308600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr13:53304800-53309000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr13:53305000-53309000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr13:53305200-53309000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr13:53305400-53308400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr13:53306200-53310600	Weak transcription	H9 Cell Line	embryonic stem cell

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