Variant report

Variant	rs6748577
Chromosome Location	chr2:113351762-113351763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113238355..113239872-chr2:113348912..113351781,2	MCF-7	breast:
2	chr2:113350147..113353679-chr2:113358918..113360716,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10171686	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10190108	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691929	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11694460	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11694966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469092	0.91[ASN][1000 genomes]
rs12477807	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12611573	0.94[ASN][1000 genomes]
rs12613849	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34725617	0.85[EUR][1000 genomes]
rs3849317	0.83[JPT][hapmap]
rs3961913	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4848284	0.83[JPT][hapmap]
rs6749723	0.98[ASN][1000 genomes]
rs6757781	0.83[JPT][hapmap]
rs7594007	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606487	0.99[ASN][1000 genomes]
rs934748	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs934749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6748577	EDAR	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113343200-113353000	Weak transcription	NH-A	brain
2	chr2:113343200-113357400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:113343200-113357400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:113343200-113357400	Weak transcription	A549	lung
5	chr2:113343200-113357400	Weak transcription	HMEC	breast
6	chr2:113343200-113357400	Weak transcription	NHDF-Ad	bronchial
7	chr2:113343400-113357400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:113343600-113357400	Weak transcription	K562	blood
9	chr2:113343600-113357600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:113343800-113357600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:113344200-113360800	Weak transcription	Fetal Brain Male	brain
12	chr2:113344800-113357600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:113345200-113352400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:113345200-113357400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:113345200-113357600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:113345400-113357600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:113346400-113353400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:113346400-113357600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:113346400-113357600	Weak transcription	Liver	Liver
20	chr2:113346400-113357600	Weak transcription	Brain Angular Gyrus	brain
21	chr2:113346400-113357600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:113346400-113357600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:113346400-113357600	Weak transcription	Fetal Kidney	kidney
24	chr2:113346800-113354000	Weak transcription	Left Ventricle	heart
25	chr2:113346800-113354000	Weak transcription	Right Ventricle	heart
26	chr2:113346800-113357400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr2:113346800-113357400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:113346800-113357400	Weak transcription	Adipose Nuclei	Adipose
29	chr2:113346800-113357400	Weak transcription	Psoas Muscle	Psoas
30	chr2:113346800-113357400	Weak transcription	HepG2	liver
31	chr2:113346800-113357400	Weak transcription	Osteobl	bone
32	chr2:113346800-113357600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:113346800-113357600	Weak transcription	Brain Substantia Nigra	brain
34	chr2:113346800-113357600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:113346800-113357600	Weak transcription	Spleen	Spleen
36	chr2:113346800-113357600	Weak transcription	HSMM	muscle
37	chr2:113346800-113357600	Weak transcription	HSMMtube	muscle
38	chr2:113346800-113357600	Weak transcription	NHLF	lung
39	chr2:113346800-113374600	Weak transcription	Ovary	ovary
40	chr2:113347000-113351800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:113347200-113357400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:113347200-113357400	Weak transcription	NHEK	skin
43	chr2:113347400-113357400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:113347400-113357400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:113347400-113357600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:113347400-113357600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:113347400-113359200	Weak transcription	Brain Germinal Matrix	brain
48	chr2:113347600-113352400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:113347600-113357400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:113347600-113357400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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