Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:75273373..75275096-chr11:75428137..75429945,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP6-5	chr11:75429251-75429433	NONHSAT023119

Variant related genes	Relation type
ENSG00000149257	Chromatin interaction

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10793123	0.81[EUR][1000 genomes]
rs10899102	0.89[EUR][1000 genomes]
rs1145700	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1219536	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1219537	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1219538	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1219539	0.88[EUR][1000 genomes]
rs473013	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs473791	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs554202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623693	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650861	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897924	chr11:75424546-75678647	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1238914	LRRC32	cis	parietal	SCAN
rs1238914	GAB2	cis	parietal	SCAN
rs1238914	NUMA1	cis	parietal	SCAN
rs1238914	ARHGEF17	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75427200-75429400	Enhancers	HepG2	liver
2	chr11:75428000-75429600	Enhancers	Liver	Liver
3	chr11:75428200-75431200	Enhancers	Gastric	stomach
4	chr11:75428400-75429400	Active TSS	Colonic Mucosa	Colon
5	chr11:75428600-75430200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:75428600-75430600	Active TSS	Duodenum Mucosa	Duodenum
7	chr11:75428600-75431000	Enhancers	Stomach Mucosa	stomach
8	chr11:75428800-75429600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:75428800-75429600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:75428800-75430000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr11:75428800-75430200	Enhancers	Right Ventricle	heart
12	chr11:75428800-75430400	Enhancers	Adipose Nuclei	Adipose
13	chr11:75428800-75431000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:75428800-75431000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr11:75428800-75431200	Enhancers	Left Ventricle	heart
16	chr11:75428800-75431200	Active TSS	Rectal Smooth Muscle	rectum
17	chr11:75429000-75429800	Enhancers	Right Atrium	heart
18	chr11:75429000-75430200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr11:75429000-75430400	Enhancers	Fetal Heart	heart
20	chr11:75429000-75431600	Flanking Active TSS	Fetal Intestine Large	intestine
21	chr11:75429000-75431600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr11:75429200-75429400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
23	chr11:75429200-75429800	Active TSS	Small Intestine	intestine

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