Variant report

Variant	rs555306
Chromosome Location	chr11:71854493-71854494
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:71848622..71850667-chr11:71854281..71856804,2	MCF-7	breast:
2	chr11:71817497..71819718-chr11:71852568..71855106,2	MCF-7	breast:
3	chr11:71821717..71826052-chr11:71851780..71856774,7	MCF-7	breast:
4	chr11:71822348..71825348-chr11:71852319..71854832,3	MCF-7	breast:
5	chr11:71850218..71852679-chr11:71853502..71855781,2	MCF-7	breast:
6	chr11:71853234..71854961-chr11:71893001..71894509,2	MCF-7	breast:
7	chr11:71853125..71854944-chr11:71891324..71892926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110203	Chromatin interaction
ENSG00000110200	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10751196	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10751197	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10793020	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2212468	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508867	0.90[ASN][1000 genomes]
rs28490487	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4081422	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap]
rs4341566	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4430545	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4630325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520360	0.88[ASN][1000 genomes]
rs550638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58949519	0.83[ASN][1000 genomes]
rs590586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59684857	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs619237	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs649089	0.88[ASN][1000 genomes]
rs667351	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs670507	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs682244	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7949807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv1054858	chr11:71847797-71880291	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3493111	chr11:71850822-71893073	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3493112	chr11:71850822-71893073	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv435918	chr11:71851427-71890983	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv5948	chr11:71851479-71890582	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv3359634	chr11:71851533-71892403	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv2513904	chr11:71852934-71892793	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs555306	C7orf25	trans	multi-tissue	Pritchard
rs555306	CTRB2	trans	multi-tissue	Pritchard
rs555306	C8orf13	trans	multi-tissue	Pritchard
rs555306	FOLR1	cis	multi-tissue	Pritchard
rs555306	FOLR3	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71848400-71854600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:71850800-71856200	Enhancers	HMEC	breast
3	chr11:71851200-71856200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:71852200-71854800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:71852800-71855000	Weak transcription	A549	lung
6	chr11:71853000-71856200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:71853200-71854800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr11:71853200-71855400	Weak transcription	NHLF	lung
9	chr11:71853400-71854800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr11:71853400-71854800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:71853400-71854800	Weak transcription	NHDF-Ad	bronchial
12	chr11:71853400-71855000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:71853400-71855200	Weak transcription	NH-A	brain
14	chr11:71853400-71855400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:71853400-71856000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:71853400-71856400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:71853600-71854800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:71853600-71854800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:71853600-71854800	Weak transcription	Hela-S3	cervix
20	chr11:71853600-71855400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:71853800-71856600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:71854200-71855200	Enhancers	Fetal Thymus	thymus
23	chr11:71854200-71856000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:71854400-71854600	ZNF genes & repeats	HSMM	muscle
25	chr11:71854400-71855400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr11:71854400-71856200	Genic enhancers	NHEK	skin
27	chr11:71854400-71856400	Enhancers	Osteobl	bone
28	chr11:71854400-71857000	Enhancers	Placenta	Placenta

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