Variant report

Variant	rs598936
Chromosome Location	chr11:75100600-75100601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75098909..75103589-chr11:75108306..75112041,8	MCF-7	breast:
2	chr11:75053704..75056779-chr11:75098443..75101386,3	MCF-7	breast:
3	chr11:75098442..75101269-chr11:75243571..75246252,2	K562	blood:
4	chr11:75098397..75102826-chr11:75109397..75111957,5	MCF-7	breast:
5	chr11:75099655..75101475-chr11:75264978..75266737,2	K562	blood:

Variant related genes	Relation type
ENSG00000206941	Chromatin interaction
ENSG00000149273	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11236417	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11236420	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12363921	0.85[ASN][1000 genomes]
rs3016302	0.88[ASN][1000 genomes]
rs3016304	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs473233	0.88[ASN][1000 genomes]
rs473961	0.88[ASN][1000 genomes]
rs475099	0.84[ASN][1000 genomes]
rs475161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs477625	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs477783	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs478777	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs489691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs515343	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521455	0.87[ASN][1000 genomes]
rs532279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs536516	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs536538	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs542784	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs542944	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs542994	0.85[CEU][hapmap]
rs546715	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552129	0.88[ASN][1000 genomes]
rs555875	1.00[JPT][hapmap]
rs567647	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs575781	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576508	0.88[ASN][1000 genomes]
rs580152	0.95[ASN][1000 genomes]
rs598062	0.96[ASN][1000 genomes]
rs613248	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs613690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs627133	0.89[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs629991	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs630429	0.80[ASN][1000 genomes]
rs646360	0.84[ASN][1000 genomes]
rs654079	0.85[ASN][1000 genomes]
rs663235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs672534	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs686020	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
2	nsv832211	chr11:74945839-75106125	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
3	nsv897920	chr11:75087520-75181249	Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs598936	KCNE3	cis	parietal	SCAN
rs598936	IL18BP	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75098000-75100600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr11:75098200-75101200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:75099000-75100600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:75099400-75100600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:75099400-75100600	Enhancers	Fetal Lung	lung
6	chr11:75099600-75100600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr11:75099800-75100600	Enhancers	K562	blood
8	chr11:75100200-75100600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:75100200-75110200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:75100400-75100600	Enhancers	Hela-S3	cervix
11	chr11:75100400-75101800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:75100400-75105200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:75100400-75105400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:75100400-75106000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:75100400-75106000	Weak transcription	Spleen	Spleen
16	chr11:75100400-75106200	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:75100400-75106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:75100400-75110400	Weak transcription	HSMMtube	muscle
19	chr11:75100600-75101800	Weak transcription	Hela-S3	cervix
20	chr11:75100600-75105400	Weak transcription	K562	blood
21	chr11:75100600-75110400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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