Variant report

Variant	rs10804492
Chromosome Location	chr3:111457016-111457017
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	chr3:111456141..111458585-chr3:111526075..111527610,2	MCF-7	breast:
2	chr3:111452923..111457246-chr3:111577346..111581538,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11711582	0.81[CHD][hapmap]
rs11922220	0.85[CEU][hapmap]
rs11929568	0.88[ASW][hapmap];0.89[LWK][hapmap]
rs12490337	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12495513	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12632878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355769	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325897	0.85[CEU][hapmap]
rs4557129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682299	0.81[CHD][hapmap]
rs4682302	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438003	0.81[CHD][hapmap]
rs6782962	0.90[CEU][hapmap]
rs6784441	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6788543	0.81[CHD][hapmap]
rs6794420	0.89[LWK][hapmap]
rs6796087	0.81[CHD][hapmap]
rs6796976	0.89[LWK][hapmap]
rs6801225	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629156	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]
rs955382	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10804492	SAT2	trans	parietal	SCAN
rs10804492	CD200	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111452400-111458800	Enhancers	HMEC	breast
4	chr3:111452600-111457200	Enhancers	HSMM	muscle
5	chr3:111452800-111459200	Enhancers	Osteobl	bone
6	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:111453400-111458600	Enhancers	HSMMtube	muscle
9	chr3:111453600-111458800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:111453600-111458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
12	chr3:111453800-111457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:111453800-111457600	Enhancers	NHEK	skin
14	chr3:111454200-111458200	Enhancers	Hela-S3	cervix
15	chr3:111454600-111458000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:111454600-111459400	Enhancers	HepG2	liver
17	chr3:111454600-111459600	Enhancers	Liver	Liver
18	chr3:111454800-111460400	Enhancers	Fetal Heart	heart
19	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
20	chr3:111455000-111457600	Weak transcription	HUVEC	blood vessel
21	chr3:111455000-111461000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr3:111455600-111458600	Enhancers	Right Atrium	heart
23	chr3:111455600-111458800	Enhancers	Adipose Nuclei	Adipose
24	chr3:111455800-111457200	Enhancers	Fetal Stomach	stomach
25	chr3:111455800-111458400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:111455800-111458400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:111455800-111458600	Enhancers	Psoas Muscle	Psoas
28	chr3:111455800-111458800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:111455800-111459000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:111455800-111459200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:111455800-111461000	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:111456000-111457600	Enhancers	Fetal Lung	lung
33	chr3:111456000-111458200	Enhancers	Colon Smooth Muscle	Colon
34	chr3:111456000-111458600	Enhancers	Stomach Smooth Muscle	stomach
35	chr3:111456000-111458800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:111456000-111459000	Enhancers	Fetal Muscle Leg	muscle
37	chr3:111456000-111459000	Enhancers	Stomach Mucosa	stomach
38	chr3:111456200-111457200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:111456200-111457400	Enhancers	Fetal Kidney	kidney
40	chr3:111456200-111459000	Flanking Active TSS	A549	lung
41	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
42	chr3:111456400-111457200	Enhancers	GM12878-XiMat	blood
43	chr3:111456400-111457600	Weak transcription	Left Ventricle	heart
44	chr3:111456400-111457600	Weak transcription	Ovary	ovary
45	chr3:111456400-111457600	Weak transcription	Pancreas	Pancrea
46	chr3:111456400-111457600	Weak transcription	Right Ventricle	heart
47	chr3:111456400-111458200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:111456400-111458400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:111456400-111459000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:111456400-111459000	Weak transcription	Gastric	stomach

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