Variant report

Variant	rs2501618
Chromosome Location	chr1:179958809-179958810
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	chr1:179947029..179952263-chr1:179955680..179959791,6	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10913916	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10913917	0.94[JPT][hapmap]
rs10913918	0.87[JPT][hapmap];0.81[MKK][hapmap]
rs12075450	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs12091685	0.85[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs1281384	0.87[JPT][hapmap]
rs1281389	0.87[JPT][hapmap]
rs16855164	0.88[ASN][1000 genomes]
rs1981314	0.86[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2281805	0.87[JPT][hapmap]
rs2319676	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2319677	0.84[CEU][hapmap]
rs2477106	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477107	0.89[ASN][1000 genomes]
rs2477109	0.96[ASN][1000 genomes]
rs2477111	0.94[JPT][hapmap]
rs2477112	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2477113	0.98[ASN][1000 genomes]
rs2477115	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477117	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2477118	0.94[JPT][hapmap]
rs2477119	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2483622	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501607	0.88[JPT][hapmap]
rs2501608	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501611	0.94[JPT][hapmap]
rs2501613	0.94[JPT][hapmap]
rs2501614	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501615	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2501617	0.88[JPT][hapmap]
rs2501619	0.97[ASN][1000 genomes]
rs2501621	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2762859	0.94[JPT][hapmap]
rs3123521	0.92[ASN][1000 genomes]
rs3767201	0.86[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs4147170	0.84[CEU][hapmap]
rs4263962	0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4379644	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4622030	0.84[CEU][hapmap]
rs4651055	0.97[CHD][hapmap];0.87[JPT][hapmap]
rs4652461	1.00[ASW][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs483307	0.94[JPT][hapmap]
rs504202	0.87[JPT][hapmap]
rs510209	0.94[JPT][hapmap]
rs521858	0.87[JPT][hapmap]
rs526683	0.93[JPT][hapmap]
rs533795	0.87[JPT][hapmap]
rs551607	0.81[ASW][hapmap];0.87[JPT][hapmap]
rs552743	0.87[JPT][hapmap]
rs561233	0.87[JPT][hapmap]
rs6425602	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425606	0.90[ASW][hapmap];0.84[CEU][hapmap]
rs6425607	0.84[CEU][hapmap]
rs6659911	0.84[ASN][1000 genomes]
rs6660984	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs6676989	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682558	0.83[CEU][hapmap]
rs6692394	0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7521895	0.87[JPT][hapmap]
rs7521948	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425852	0.85[ASN][1000 genomes]
rs9425853	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425857	0.80[ASN][1000 genomes]
rs9425859	0.91[CHD][hapmap]
rs9887843	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179926800-179961400	Weak transcription	A549	lung
3	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:179938600-179959000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:179938600-179965800	Weak transcription	Esophagus	oesophagus
7	chr1:179938600-179975800	Weak transcription	Thymus	Thymus
8	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179938600-179984600	Weak transcription	Lung	lung
10	chr1:179938800-179959800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:179939000-179989000	Weak transcription	Gastric	stomach
12	chr1:179939800-179959400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:179939800-179974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:179940000-179961200	Weak transcription	HSMM	muscle
15	chr1:179941000-179959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
17	chr1:179946400-179959000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:179946400-179959000	Weak transcription	Right Ventricle	heart
19	chr1:179946400-179959200	Weak transcription	Osteobl	bone
20	chr1:179946400-179963200	Weak transcription	HUVEC	blood vessel
21	chr1:179946400-179965600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:179946400-179972800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:179946400-179983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:179946400-179989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:179946600-179961200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:179946600-179961400	Weak transcription	HepG2	liver
27	chr1:179946600-179965800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:179946600-179965800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:179946600-179983200	Weak transcription	Brain Angular Gyrus	brain
30	chr1:179946800-179959200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:179946800-179959200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:179946800-179963800	Weak transcription	Adipose Nuclei	Adipose
33	chr1:179947800-179989400	Weak transcription	Small Intestine	intestine
34	chr1:179948000-179961200	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:179948400-179965800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:179948400-179971800	Weak transcription	Fetal Heart	heart
37	chr1:179948600-179983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:179949200-179961200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:179949200-179963800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:179949400-179980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:179950000-179980600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:179950200-179966000	Weak transcription	Fetal Brain Female	brain
43	chr1:179951400-179972200	Weak transcription	Psoas Muscle	Psoas
44	chr1:179951400-179974600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:179951800-179974800	Weak transcription	Hela-S3	cervix
46	chr1:179952400-179965600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:179953200-179960000	Weak transcription	Right Atrium	heart
48	chr1:179953400-179965400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:179953600-179959800	Weak transcription	Placenta	Placenta
50	chr1:179953600-179964800	Weak transcription	Muscle Satellite Cultured Cells	--

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