Variant report

Variant	rs17597893
Chromosome Location	chr18:12812061-12812062
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	chr18:12810815..12813170-chr18:12815454..12817279,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10502414	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10502415	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1065630	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16939859	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17598047	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17656120	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17656142	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17657106	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs2847288	0.90[CEU][hapmap]
rs45458596	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs45506596	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45510799	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45518232	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45518540	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45575332	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45602843	0.90[EUR][1000 genomes]
rs45626137	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57450722	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57528860	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59368414	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59698881	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60617398	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73402502	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73404411	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73404414	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404420	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404421	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404424	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404453	0.91[EUR][1000 genomes]
rs73414061	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8084006	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8085163	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8088256	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs8092305	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs973767	0.89[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
8	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767400-12815800	Weak transcription	Gastric	stomach
2	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
4	chr18:12787600-12815800	Weak transcription	Pancreas	Pancrea
5	chr18:12789000-12821400	Weak transcription	Small Intestine	intestine
6	chr18:12789200-12814200	Weak transcription	Fetal Kidney	kidney
7	chr18:12790200-12828000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr18:12790400-12813600	Weak transcription	A549	lung
9	chr18:12790400-12814000	Weak transcription	Osteobl	bone
10	chr18:12790400-12815800	Weak transcription	K562	blood
11	chr18:12790600-12820000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:12791200-12815800	Weak transcription	Brain Germinal Matrix	brain
13	chr18:12791200-12819600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr18:12791400-12819600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
16	chr18:12791600-12828000	Weak transcription	HUVEC	blood vessel
17	chr18:12791800-12821600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:12792200-12815800	Weak transcription	NH-A	brain
19	chr18:12792800-12815800	Weak transcription	Brain Angular Gyrus	brain
20	chr18:12792800-12819600	Weak transcription	NHLF	lung
21	chr18:12794600-12815800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr18:12795200-12815800	Weak transcription	Brain Anterior Caudate	brain
23	chr18:12797800-12819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr18:12798000-12814800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr18:12798200-12814200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr18:12798200-12814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr18:12801200-12815600	Weak transcription	HepG2	liver
28	chr18:12801400-12813600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr18:12801800-12812400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:12801800-12815600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr18:12802200-12812200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:12802200-12813200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:12802200-12814400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr18:12802400-12812600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr18:12803600-12813200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr18:12804000-12813800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr18:12804000-12814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr18:12805000-12812800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:12806400-12816600	Strong transcription	Primary B cells from cord blood	blood
41	chr18:12806400-12827600	Strong transcription	Dnd41	blood
42	chr18:12806800-12827400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr18:12807000-12815400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:12807000-12815600	Weak transcription	Fetal Brain Female	brain
45	chr18:12807200-12819600	Weak transcription	Brain Substantia Nigra	brain
46	chr18:12807200-12826600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
48	chr18:12807400-12816000	Weak transcription	Fetal Brain Male	brain
49	chr18:12807400-12821400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr18:12807800-12817400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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