Variant report

Variant	rs12416804
Chromosome Location	chr11:72048526-72048527
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72043541..72046413-chr11:72048460..72050772,2	MCF-7	breast:
2	chr11:72032928..72035101-chr11:72048311..72049963,2	K562	blood:
3	chr11:72047915..72051506-chr11:72051775..72054985,4	K562	blood:
4	chr11:72048175..72050964-chr11:72057848..72059463,2	K562	blood:
5	chr11:72047802..72049631-chr11:72136016..72138131,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10501410	0.88[CEU][hapmap]
rs12416741	0.82[MEX][hapmap]
rs12418637	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421674	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17162126	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784257	0.82[MEX][hapmap]
rs2508201	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2508865	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3750906	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3900852	0.94[MEX][hapmap];0.85[TSI][hapmap]
rs472837	0.81[MEX][hapmap]
rs474629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs504217	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55721826	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55930012	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56076328	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56171963	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58044536	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58941166	0.80[EUR][1000 genomes]
rs58945323	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590732	0.82[MEX][hapmap]
rs60081894	0.89[EUR][1000 genomes]
rs61036532	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680660	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73528886	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73530718	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73530724	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530754	0.91[EUR][1000 genomes]
rs73530756	0.91[EUR][1000 genomes]
rs73530785	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7940062	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv832206	chr11:72006573-72176017	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv1794740	chr11:72021720-72332931	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12416804	FOLR3	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72012800-72070600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr11:72025600-72054000	Weak transcription	GM12878-XiMat	blood
3	chr11:72026600-72067400	Weak transcription	Fetal Intestine Large	intestine
4	chr11:72027600-72060600	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:72028400-72060800	Weak transcription	Gastric	stomach
6	chr11:72030600-72060200	Weak transcription	Adipose Nuclei	Adipose
7	chr11:72032800-72054600	Weak transcription	Brain Anterior Caudate	brain
8	chr11:72033000-72075600	Weak transcription	A549	lung
9	chr11:72033200-72063800	Weak transcription	Aorta	Aorta
10	chr11:72038200-72071200	Weak transcription	HMEC	breast
11	chr11:72038400-72049800	Weak transcription	NHDF-Ad	bronchial
12	chr11:72038400-72053600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:72038400-72076600	Weak transcription	Liver	Liver
14	chr11:72038800-72060600	Weak transcription	Esophagus	oesophagus
15	chr11:72039400-72060400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:72039600-72049400	Weak transcription	HSMMtube	muscle
17	chr11:72039800-72077400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:72040000-72060200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:72040000-72070800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr11:72040400-72049600	Weak transcription	Spleen	Spleen
21	chr11:72040400-72053800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:72040400-72060600	Weak transcription	Ovary	ovary
23	chr11:72040400-72069400	Weak transcription	Fetal Brain Female	brain
24	chr11:72040800-72070800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr11:72041000-72060200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:72041200-72054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:72041400-72049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:72041400-72064600	Weak transcription	Hela-S3	cervix
29	chr11:72041600-72050200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:72041600-72060600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:72041800-72049200	Weak transcription	Left Ventricle	heart
32	chr11:72041800-72049600	Weak transcription	Dnd41	blood
33	chr11:72041800-72060600	Weak transcription	Psoas Muscle	Psoas
34	chr11:72041800-72063600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:72041800-72067400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:72041800-72072200	Weak transcription	HUVEC	blood vessel
37	chr11:72041800-72076000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:72042000-72059800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:72043200-72076600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr11:72044800-72053400	Weak transcription	HepG2	liver
41	chr11:72044800-72063600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:72045000-72049000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:72045000-72060800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:72045200-72049400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:72045200-72049800	Weak transcription	Osteobl	bone
46	chr11:72045200-72060400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:72045400-72049600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:72045600-72060600	Weak transcription	Thymus	Thymus
49	chr11:72045600-72061000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:72045600-72065200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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