Variant report

Variant	rs2576180
Chromosome Location	chr10:90234745-90234746
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:90196554..90197353-chr10:90234056..90234795,2	MCF-7	breast:
2	chr10:90233064..90234940-chr11:69455221..69456769,2	MCF-7	breast:
3	chr10:90234207..90234776-chr10:90285280..90285826,2	MCF-7	breast:
4	chr10:90144173..90146300-chr10:90233140..90235508,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110092	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10749586	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10749587	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10749588	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10788604	0.97[ASN][1000 genomes]
rs10788605	0.97[ASN][1000 genomes]
rs10887827	0.97[ASN][1000 genomes]
rs10887829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11202750	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1177587	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1183901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325903	0.84[CHB][hapmap]
rs1325907	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1359580	0.85[CHB][hapmap]
rs1409134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1925937	0.88[AMR][1000 genomes]
rs1935578	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1952122	0.84[CHB][hapmap]
rs1980812	0.88[AMR][1000 genomes]
rs2077890	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2153856	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2437871	0.84[CHB][hapmap];0.88[AMR][1000 genomes]
rs2437872	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2437874	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2437877	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2437878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2477952	0.87[AMR][1000 genomes]
rs2477955	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2477957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488271	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576166	0.84[CHB][hapmap];0.88[AMR][1000 genomes]
rs2576174	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2576179	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2765441	0.82[AFR][1000 genomes]
rs2765442	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2765444	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2986118	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4403718	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs725683	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725684	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs745354	0.85[CHB][hapmap]
rs7902230	0.97[ASN][1000 genomes]
rs7904229	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7916937	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7917100	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90227600-90237000	Weak transcription	Left Ventricle	heart
2	chr10:90233000-90236000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:90233800-90239200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr10:90234000-90234800	Enhancers	Rectal Smooth Muscle	rectum
5	chr10:90234000-90234800	Enhancers	Small Intestine	intestine
6	chr10:90234000-90235000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr10:90234000-90235200	Enhancers	NHEK	skin
8	chr10:90234000-90235400	Enhancers	Hela-S3	cervix
9	chr10:90234000-90235600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:90234000-90235600	Enhancers	Liver	Liver
11	chr10:90234000-90235600	Enhancers	Ovary	ovary
12	chr10:90234200-90235000	Enhancers	Colon Smooth Muscle	Colon
13	chr10:90234200-90235400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:90234200-90235600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr10:90234200-90236000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr10:90234400-90234800	Weak transcription	Aorta	Aorta
17	chr10:90234400-90234800	Weak transcription	Pancreas	Pancrea
18	chr10:90234400-90235000	Enhancers	Stomach Mucosa	stomach
19	chr10:90234400-90235200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:90234400-90235400	Enhancers	Fetal Heart	heart
21	chr10:90234400-90235600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr10:90234400-90235600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:90234400-90238200	Weak transcription	Right Ventricle	heart
24	chr10:90234600-90235000	Enhancers	Psoas Muscle	Psoas
25	chr10:90234600-90235000	Enhancers	Right Atrium	heart
26	chr10:90234600-90235000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr10:90234600-90235000	Flanking Active TSS	HMEC	breast
28	chr10:90234600-90235200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr10:90234600-90235200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr10:90234600-90235600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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