Variant report

Variant	rs11236401
Chromosome Location	chr11:75068767-75068768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75067230..75070089-chr11:75082011..75083842,2	MCF-7	breast:
2	chr11:75061810..75065838-chr11:75066153..75069996,4	MCF-7	breast:
3	chr11:75067548..75069783-chr11:75074663..75077055,2	MCF-7	breast:
4	chr11:75060264..75064517-chr11:75067052..75070249,4	MCF-7	breast:
5	chr11:75065936..75068463-chr11:75068645..75070545,2	K562	blood:

Variant related genes	Relation type
ENSG00000137486	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10899087	0.95[ASN][1000 genomes]
rs11236397	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236398	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11236405	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236407	0.85[CEU][hapmap]
rs11236416	0.86[AMR][1000 genomes]
rs11602596	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269895	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270766	0.86[AMR][1000 genomes]
rs12271518	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12271945	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs12278108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12291595	0.93[CEU][hapmap];0.86[AMR][1000 genomes]
rs12577286	0.95[ASN][1000 genomes]
rs12794577	0.86[AMR][1000 genomes]
rs12797588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34530827	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121885	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7101921	0.83[AMR][1000 genomes]
rs7116977	0.83[AMR][1000 genomes]
rs7120396	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs73004237	0.83[AMR][1000 genomes]
rs7929742	0.95[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	nsv522447	chr11:74982939-75068767	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11236401	GDPD4	cis	cerebellum	SCAN
rs11236401	C2CD3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75063600-75076800	Weak transcription	Hela-S3	cervix
2	chr11:75064200-75086800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:75064600-75071800	Weak transcription	Primary B cells from cord blood	blood
4	chr11:75066600-75076000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:75067000-75068800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:75067200-75076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:75067400-75069000	Enhancers	HUVEC	blood vessel
8	chr11:75067600-75068800	Enhancers	Spleen	Spleen
9	chr11:75067600-75069000	Enhancers	Fetal Muscle Leg	muscle
10	chr11:75068000-75068800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:75068000-75069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:75068600-75068800	Enhancers	Lung	lung

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