Variant report

Variant	rs12187407
Chromosome Location	chr5:179928383-179928384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179926447..179929444-chr5:180030197..180034087,3	MCF-7	breast:
2	chr5:179928152..179929958-chr6:152022823..152024616,2	MCF-7	breast:
3	chr5:179922992..179929395-chr5:179931202..179936163,8	K562	blood:
4	chr5:179926836..179929553-chr5:179936130..179939014,2	MCF-7	breast:
5	chr5:179928367..179929867-chr8:141667673..141670357,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10464103	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516143	0.83[EUR][1000 genomes]
rs10516144	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10516145	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10903256	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10903257	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10903261	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1105972	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249716	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249717	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249718	0.87[ASN][1000 genomes]
rs11249719	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249720	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11249722	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249723	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249725	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249726	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249728	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249729	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11249731	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249732	0.92[EUR][1000 genomes]
rs11738044	0.83[EUR][1000 genomes]
rs11738129	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11738199	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11740950	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742093	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11743298	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11748611	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748880	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11750412	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11750506	0.83[EUR][1000 genomes]
rs11949971	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11956294	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054820	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12188182	0.83[EUR][1000 genomes]
rs13152935	0.81[ASN][1000 genomes]
rs13154251	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155576	0.85[EUR][1000 genomes]
rs13164926	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13165676	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13166941	0.84[EUR][1000 genomes]
rs13168301	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13168976	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13169807	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171802	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13172721	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13174261	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13175241	1.00[ASN][1000 genomes]
rs13181218	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182715	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13185177	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13185444	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190607	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13361838	0.94[ASN][1000 genomes]
rs1478360	0.92[EUR][1000 genomes]
rs1994912	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2131811	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2387283	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2387284	0.82[EUR][1000 genomes]
rs2387287	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387288	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617262	0.97[ASN][1000 genomes]
rs34294053	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35710030	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4002641	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405497	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62405523	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405524	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405545	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601127	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6601129	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67607816	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6859296	0.83[EUR][1000 genomes]
rs6864038	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6874985	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6879011	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887532	0.90[ASN][1000 genomes]
rs6888064	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894846	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6897365	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704287	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7705358	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7705421	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705521	0.90[EUR][1000 genomes]
rs7722020	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724243	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7726226	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727679	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937919	1.00[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	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179923000-179934600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:179923200-179928400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr5:179923200-179936400	Weak transcription	Fetal Intestine Large	intestine
4	chr5:179923400-179946000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:179923600-179928600	Weak transcription	HUVEC	blood vessel
6	chr5:179923600-179929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:179923600-179930400	Weak transcription	NHLF	lung
8	chr5:179923600-179931200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr5:179923600-179932800	Weak transcription	Right Ventricle	heart
10	chr5:179923600-179933400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:179923600-179933800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:179923600-179934400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:179923600-179934400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:179923600-179942000	Weak transcription	Spleen	Spleen
15	chr5:179923600-179949800	Weak transcription	Gastric	stomach
16	chr5:179923600-179949800	Weak transcription	Psoas Muscle	Psoas
17	chr5:179923600-179957000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:179923800-179928600	Weak transcription	Fetal Kidney	kidney
19	chr5:179923800-179929200	Weak transcription	NHDF-Ad	bronchial
20	chr5:179923800-179931000	Weak transcription	Osteobl	bone
21	chr5:179923800-179932800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:179923800-179933000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr5:179923800-179934600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:179923800-179935400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:179923800-179941200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:179924000-179928600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:179924000-179933000	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:179924000-179933400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:179924000-179934600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:179924000-179934600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:179924000-179935200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:179924000-179948000	Weak transcription	A549	lung
33	chr5:179924000-179949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:179924200-179933400	Weak transcription	Fetal Heart	heart
35	chr5:179924200-179949200	Weak transcription	Pancreas	Pancrea
36	chr5:179924200-179949600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:179924200-179950000	Weak transcription	Brain Angular Gyrus	brain
38	chr5:179924400-179928600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:179924400-179933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:179924600-179930000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:179924600-179930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:179924600-179934000	Weak transcription	HSMM	muscle
43	chr5:179924600-179941600	Weak transcription	Brain Germinal Matrix	brain
44	chr5:179924600-179944800	Weak transcription	Fetal Brain Male	brain
45	chr5:179924600-179944800	Weak transcription	Fetal Lung	lung
46	chr5:179924600-179949800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:179924600-179957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:179924800-179932800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr5:179925000-179929400	Strong transcription	GM12878-XiMat	blood
50	chr5:179925000-179936200	Weak transcription	Fetal Muscle Trunk	muscle

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