Variant report

Variant	rs12120187
Chromosome Location	chr1:79126050-79126051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493615	0.84[EUR][1000 genomes]
rs1107320	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109244	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162523	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162536	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162537	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162539	0.85[EUR][1000 genomes]
rs11162540	0.85[EUR][1000 genomes]
rs11162541	0.85[EUR][1000 genomes]
rs11162544	0.84[EUR][1000 genomes]
rs11577395	0.87[CHB][hapmap];0.83[CHD][hapmap];0.91[TSI][hapmap]
rs11587990	0.85[EUR][1000 genomes]
rs12128384	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403117	0.85[EUR][1000 genomes]
rs12409331	0.85[EUR][1000 genomes]
rs12409781	0.85[EUR][1000 genomes]
rs17395034	0.85[EUR][1000 genomes]
rs17395097	0.84[EUR][1000 genomes]
rs17398682	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17399158	0.84[EUR][1000 genomes]
rs17399192	0.84[EUR][1000 genomes]
rs1887286	0.84[EUR][1000 genomes]
rs1926897	0.84[EUR][1000 genomes]
rs1926898	0.84[EUR][1000 genomes]
rs1926901	0.87[EUR][1000 genomes]
rs1926902	0.85[EUR][1000 genomes]
rs1926903	0.85[EUR][1000 genomes]
rs1926904	0.85[EUR][1000 genomes]
rs1926905	0.85[EUR][1000 genomes]
rs273250	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58150654	0.85[EUR][1000 genomes]
rs58830966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58921479	0.85[EUR][1000 genomes]
rs58945140	0.85[EUR][1000 genomes]
rs58993850	0.85[EUR][1000 genomes]
rs59409549	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60311076	0.85[EUR][1000 genomes]
rs61500835	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61613596	0.85[EUR][1000 genomes]
rs61681700	0.85[EUR][1000 genomes]
rs61769988	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769992	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61769996	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61770023	0.85[EUR][1000 genomes]
rs61770024	0.85[EUR][1000 genomes]
rs6669498	0.87[CHB][hapmap]
rs6678067	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546403	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975986	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975987	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79116000-79128600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:79116400-79127200	Weak transcription	Fetal Intestine Large	intestine
3	chr1:79116400-79129000	Weak transcription	Placenta	Placenta
4	chr1:79116400-79130000	Weak transcription	Stomach Mucosa	stomach
5	chr1:79117000-79132800	Weak transcription	Fetal Brain Male	brain
6	chr1:79117400-79126800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:79117400-79128400	Weak transcription	HSMMtube	muscle
8	chr1:79117400-79129800	Weak transcription	NHLF	lung
9	chr1:79117400-79130400	Weak transcription	Pancreas	Pancrea
10	chr1:79117400-79130600	Weak transcription	Hela-S3	cervix
11	chr1:79117400-79131200	Weak transcription	HSMM	muscle
12	chr1:79117400-79144000	Weak transcription	Esophagus	oesophagus
13	chr1:79117400-79144000	Weak transcription	Spleen	Spleen
14	chr1:79117600-79127000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:79117600-79129000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:79117600-79129400	Weak transcription	NH-A	brain
17	chr1:79117600-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:79117800-79130200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:79118200-79127400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:79118400-79127000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:79118400-79127200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:79118400-79128600	Weak transcription	Thymus	Thymus
23	chr1:79118400-79130800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:79118400-79130800	Weak transcription	Small Intestine	intestine
25	chr1:79118600-79130800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:79119200-79129400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:79119200-79130800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:79119400-79126400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:79119400-79129400	Weak transcription	Brain Germinal Matrix	brain
30	chr1:79119400-79129600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:79119400-79130400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:79119800-79128400	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:79119800-79130000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:79119800-79130800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:79119800-79130800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:79119800-79132600	Weak transcription	Right Ventricle	heart
37	chr1:79120000-79129400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:79120400-79130200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:79120600-79129200	Strong transcription	Fetal Lung	lung
40	chr1:79120600-79129400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:79120600-79130000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:79120600-79130200	Strong transcription	Liver	Liver
43	chr1:79120800-79130200	Strong transcription	Dnd41	blood
44	chr1:79121000-79129600	Weak transcription	Psoas Muscle	Psoas
45	chr1:79121200-79127800	Weak transcription	Left Ventricle	heart
46	chr1:79121600-79130000	Weak transcription	Fetal Stomach	stomach
47	chr1:79122000-79126800	Weak transcription	Lung	lung
48	chr1:79123200-79129200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:79124200-79127600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:79124200-79129400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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