Variant report

Variant	rs1542289
Chromosome Location	chr8:99224534-99224535
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99223225..99225357-chr8:99305724..99307688,2	MCF-7	breast:
2	chr8:99181959..99182882-chr8:99224161..99224764,2	MCF-7	breast:
3	chr8:99223515..99225249-chr8:99231760..99233868,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104361	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10093356	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10093623	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10093678	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10093856	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10095790	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10095887	0.95[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10100633	0.95[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10108460	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1109159	0.91[CEU][hapmap];0.80[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11987536	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12550682	0.89[GIH][hapmap];0.95[JPT][hapmap]
rs12677283	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12680361	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12680980	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13271095	0.89[GIH][hapmap];0.95[JPT][hapmap]
rs16896763	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16896768	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16896802	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331809	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485842	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2877460	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2877495	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735885	0.81[ASW][hapmap]
rs3735887	0.81[ASW][hapmap]
rs3779721	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734389	0.91[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4734390	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4735539	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4735540	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4735542	0.85[JPT][hapmap]
rs55908268	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56906975	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57644890	0.82[EUR][1000 genomes]
rs60414868	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6468620	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6468624	0.85[JPT][hapmap]
rs6982810	0.85[JPT][hapmap]
rs7009145	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680644	0.94[EUR][1000 genomes]
rs736191	0.87[ASW][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap];0.80[YRI][hapmap]
rs896417	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv831405	chr8:99095239-99260934	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv6326	chr8:99221674-99263687	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99191600-99243800	Weak transcription	Spleen	Spleen
2	chr8:99198200-99239200	Weak transcription	Lung	lung
3	chr8:99203800-99252600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:99205200-99259600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr8:99206600-99239800	Weak transcription	Pancreas	Pancrea
6	chr8:99208000-99227600	Weak transcription	Esophagus	oesophagus
7	chr8:99211200-99243200	Weak transcription	Fetal Lung	lung
8	chr8:99213200-99225800	Weak transcription	Fetal Heart	heart
9	chr8:99213200-99239800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:99215000-99227800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:99215400-99225000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:99215400-99227600	Weak transcription	Ovary	ovary
13	chr8:99215800-99225000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr8:99216600-99245400	Weak transcription	Stomach Mucosa	stomach
15	chr8:99216800-99224800	Weak transcription	Left Ventricle	heart
16	chr8:99217000-99229800	Weak transcription	Psoas Muscle	Psoas
17	chr8:99217000-99234400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr8:99217000-99234600	Weak transcription	Fetal Intestine Large	intestine
19	chr8:99217200-99229200	Weak transcription	Aorta	Aorta
20	chr8:99217400-99227600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr8:99217400-99238800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr8:99217800-99235000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr8:99217800-99238600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr8:99218200-99227600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr8:99218400-99259000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr8:99220600-99227600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:99220600-99234600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr8:99222400-99226000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr8:99222400-99226400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr8:99222800-99226200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:99223200-99225000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:99223400-99226200	Enhancers	NHEK	skin
33	chr8:99223400-99226400	Enhancers	NHDF-Ad	bronchial
34	chr8:99223600-99225000	Enhancers	NHLF	lung
35	chr8:99223600-99226200	Enhancers	HMEC	breast
36	chr8:99223600-99226200	Enhancers	HSMM	muscle
37	chr8:99223600-99226400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr8:99223800-99224600	Weak transcription	NH-A	brain
39	chr8:99223800-99226400	Enhancers	Osteobl	bone
40	chr8:99224000-99225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr8:99224000-99225200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:99224000-99226200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr8:99224000-99226200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr8:99224000-99227000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:99224200-99224600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:99224200-99224600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:99224200-99224600	Weak transcription	Gastric	stomach
48	chr8:99224200-99225200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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