Variant report

Variant	rs1370587
Chromosome Location	chr2:20090403-20090404
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	chr2:20089099..20091154-chr2:20092345..20094469,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10165128	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10178256	0.85[CHB][hapmap];0.80[MEX][hapmap]
rs10187524	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10190308	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10191437	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10197369	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10495700	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12477955	0.85[EUR][1000 genomes]
rs12478934	0.81[EUR][1000 genomes]
rs12612708	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12616917	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1437859	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1595414	0.85[CHB][hapmap];0.80[MEX][hapmap]
rs1947730	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2045779	0.88[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs28401180	0.84[EUR][1000 genomes]
rs28598872	0.85[EUR][1000 genomes]
rs3731663	0.85[CHB][hapmap];0.80[MEX][hapmap]
rs3820949	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs4297843	0.87[EUR][1000 genomes]
rs6721864	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6736663	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741091	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7569975	0.89[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs7572536	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7575732	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7584726	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7604699	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][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	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1370587	LOC130502	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
2	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
3	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:20075400-20097600	Weak transcription	Fetal Kidney	kidney
5	chr2:20076400-20093600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:20076400-20097200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:20076600-20097400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:20076800-20091000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:20076800-20095400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:20076800-20095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:20076800-20097200	Weak transcription	Fetal Thymus	thymus
13	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:20079200-20098600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:20079400-20097200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:20079800-20099000	Weak transcription	Thymus	Thymus
18	chr2:20081800-20095200	Weak transcription	Primary T cells from cord blood	blood
19	chr2:20083000-20095400	Weak transcription	Fetal Brain Female	brain
20	chr2:20086400-20097400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:20086600-20091200	Weak transcription	Psoas Muscle	Psoas
22	chr2:20086600-20091800	Weak transcription	Spleen	Spleen
23	chr2:20086600-20095400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:20086600-20097400	Weak transcription	HMEC	breast
25	chr2:20086600-20099800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:20087200-20097400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:20087400-20097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:20087800-20090600	Enhancers	Left Ventricle	heart
29	chr2:20088000-20091200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:20088000-20099600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:20088400-20090800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:20088400-20098200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:20088600-20090600	Enhancers	Right Ventricle	heart
34	chr2:20088800-20091800	Weak transcription	Fetal Brain Male	brain
35	chr2:20089000-20095200	Weak transcription	Dnd41	blood
36	chr2:20089000-20097200	Weak transcription	Adipose Nuclei	Adipose
37	chr2:20089200-20097200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:20089200-20097400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:20089400-20097000	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:20089400-20097200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:20089600-20090800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:20089600-20090800	Enhancers	HepG2	liver
43	chr2:20089600-20094200	Weak transcription	K562	blood
44	chr2:20089600-20097200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:20089600-20097400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:20089600-20097400	Weak transcription	NHEK	skin
47	chr2:20089600-20097600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:20089600-20098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:20089800-20090600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:20089800-20091800	Enhancers	GM12878-XiMat	blood

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