Variant report

Variant	rs2245370
Chromosome Location	chr3:100617680-100617681
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	chr3:100616771..100619471-chr3:100625186..100627247,2	MCF-7	breast:
2	chr3:100611635..100615364-chr3:100616570..100618813,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10049238	1.00[JPT][hapmap]
rs1036468	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]
rs10511180	1.00[JPT][hapmap]
rs12330346	1.00[JPT][hapmap]
rs1375510	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1449321	1.00[JPT][hapmap]
rs17338729	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs17339226	0.88[CHB][hapmap]
rs17398137	1.00[JPT][hapmap]
rs1821795	1.00[JPT][hapmap]
rs1836985	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2252229	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2304513	1.00[JPT][hapmap]
rs2576367	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2576370	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2576384	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs2576385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs2576389	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576390	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2595899	0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2713749	0.88[CHB][hapmap]
rs2713750	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2713759	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2713762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs2713794	1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs6774218	0.88[CHB][hapmap]
rs7355920	1.00[JPT][hapmap]
rs7609734	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs7625454	0.88[CHB][hapmap]
rs7641631	0.88[CHB][hapmap]
rs7646218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs7647099	1.00[JPT][hapmap]
rs7651634	1.00[JPT][hapmap]
rs9653904	1.00[JPT][hapmap]
rs9822089	1.00[JPT][hapmap]
rs9824648	1.00[JPT][hapmap]
rs9825288	1.00[JPT][hapmap]
rs9826284	1.00[JPT][hapmap]
rs9827075	1.00[JPT][hapmap]
rs9827694	1.00[JPT][hapmap]
rs9831620	1.00[JPT][hapmap]
rs9843102	1.00[JPT][hapmap]
rs9844950	1.00[JPT][hapmap]
rs9847485	1.00[JPT][hapmap]
rs9860250	1.00[JPT][hapmap]
rs9862373	1.00[JPT][hapmap]
rs9866199	1.00[JPT][hapmap]
rs9881388	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2245370	TFG	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100594400-100618200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:100599800-100618200	Weak transcription	Fetal Lung	lung
4	chr3:100610600-100619200	Weak transcription	Fetal Intestine Large	intestine
5	chr3:100612000-100622800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:100612200-100632200	Weak transcription	Fetal Stomach	stomach
7	chr3:100613000-100618200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:100613400-100618600	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:100616200-100618200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:100616800-100619400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:100617000-100617800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:100617000-100617800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:100617000-100617800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:100617000-100617800	Strong transcription	HSMMtube	muscle
15	chr3:100617000-100618000	Enhancers	Stomach Mucosa	stomach
16	chr3:100617000-100619200	Enhancers	Duodenum Mucosa	Duodenum
17	chr3:100617000-100619400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:100617000-100621200	Enhancers	Hela-S3	cervix
19	chr3:100617200-100618200	Flanking Active TSS	GM12878-XiMat	blood
20	chr3:100617200-100619000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:100617200-100621400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:100617200-100629400	Weak transcription	Ovary	ovary
23	chr3:100617400-100618000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:100617400-100618200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:100617400-100618600	Enhancers	NHEK	skin
26	chr3:100617400-100618800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:100617400-100619200	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:100617400-100622000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:100617600-100617800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:100617600-100617800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:100617600-100618000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr3:100617600-100618000	Genic enhancers	HSMM	muscle
33	chr3:100617600-100619000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:100617600-100619200	Genic enhancers	NHDF-Ad	bronchial
35	chr3:100617600-100619600	Genic enhancers	Osteobl	bone
36	chr3:100617600-100620200	Flanking Active TSS	HUVEC	blood vessel
37	chr3:100617600-100622000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:100617600-100641000	Weak transcription	Fetal Muscle Leg	muscle

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