Variant report

Variant	rs2645810
Chromosome Location	chr4:142964158-142964159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142961970..142965946-chr4:142968550..142971585,4	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13123435	0.95[ASN][1000 genomes]
rs1353603	0.81[CHD][hapmap]
rs1390989	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397736	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511251	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511252	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511256	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1845967	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858297	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908923	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908924	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645790	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645791	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645792	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645793	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645794	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645795	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645797	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645798	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645814	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667098	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667099	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667100	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667102	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2667104	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667105	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667106	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667108	0.81[CHD][hapmap]
rs2667117	0.81[CHD][hapmap]
rs336304	0.81[CHD][hapmap]
rs336306	0.90[CHD][hapmap]
rs336313	0.81[CHD][hapmap]
rs336317	0.81[CHD][hapmap]
rs336325	0.81[CHD][hapmap]
rs336330	0.90[CHD][hapmap]
rs336364	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336369	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs336371	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs336378	0.81[CHD][hapmap]
rs336379	0.81[CHD][hapmap]
rs336381	0.81[CHD][hapmap]
rs3775612	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775636	0.90[CHD][hapmap]
rs966893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830096	chr4:142867099-143023761	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428775	chr4:142943213-143050195	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2645810	FAT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142943800-142965400	Weak transcription	Aorta	Aorta
2	chr4:142945400-142983200	Weak transcription	Left Ventricle	heart
3	chr4:142947800-142977200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:142949400-142977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:142949600-142977000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:142950200-142976600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:142954600-142968400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:142956600-142977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:142956600-142977000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:142957400-142976800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:142958200-142975400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:142958400-142965000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:142958800-142964200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:142958800-142964600	Weak transcription	NHDF-Ad	bronchial
16	chr4:142958800-142964800	Weak transcription	HSMMtube	muscle
17	chr4:142959000-142968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:142959000-142977000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:142959000-142978000	Weak transcription	NHEK	skin
20	chr4:142959200-142995600	Weak transcription	Fetal Heart	heart
21	chr4:142960200-142967400	Weak transcription	Primary T cells from cord blood	blood
22	chr4:142960200-142973800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:142960600-142964400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:142961600-142976400	Weak transcription	Dnd41	blood
25	chr4:142961800-142964800	Weak transcription	HMEC	breast
26	chr4:142961800-143009600	Weak transcription	A549	lung
27	chr4:142962000-142967400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:142962200-143002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:142963000-142964800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:142963200-142965600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:142963400-143001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:142963400-143002200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:142963600-142964800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:142963600-142965600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:142964000-142965800	Enhancers	HSMM	muscle
36	chr4:142964000-142966000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:142964000-142966000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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