Variant report

Variant	rs6489159
Chromosome Location	chr12:123112806-123112807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10734924	0.95[CEU][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10744275	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10773208	0.90[CEU][hapmap];0.97[TSI][hapmap]
rs10773302	0.87[EUR][1000 genomes]
rs10846921	0.86[TSI][hapmap]
rs10846978	0.90[CEU][hapmap];0.97[TSI][hapmap]
rs10847179	0.95[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs10847415	0.84[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs10998	0.95[CEU][hapmap];0.92[TSI][hapmap]
rs11058226	0.85[TSI][hapmap]
rs1392236	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1473553	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs2062506	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2173628	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2342082	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803005	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4319547	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61954972	0.86[EUR][1000 genomes]
rs61954973	0.86[EUR][1000 genomes]
rs6416298	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6489071	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6489156	0.95[CEU][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6489157	0.95[CEU][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7295397	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7301515	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]
rs7307735	0.95[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7309390	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7314638	0.90[CEU][hapmap];0.97[TSI][hapmap]
rs7316149	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7316734	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7397990	0.95[CEU][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7954006	0.82[CEU][hapmap]
rs7955203	0.84[EUR][1000 genomes]
rs7964138	0.88[TSI][hapmap]
rs7966094	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7972728	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9705654	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9988963	0.95[CEU][hapmap];0.83[MEX][hapmap]

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	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases
2	nsv1054458	chr12:123045662-123133545	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv2761772	chr12:123045674-123115508	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123012400-123114000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123012400-123117000	Weak transcription	Pancreas	Pancrea
3	chr12:123012400-123121200	Weak transcription	Aorta	Aorta
4	chr12:123013400-123120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:123015600-123115000	Strong transcription	Dnd41	blood
6	chr12:123022600-123113800	Weak transcription	Colonic Mucosa	Colon
7	chr12:123037200-123113000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:123038400-123120000	Weak transcription	Small Intestine	intestine
9	chr12:123043800-123121800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:123050800-123115200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:123059400-123119000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:123060200-123113000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:123077400-123137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:123077600-123115000	Weak transcription	Esophagus	oesophagus
15	chr12:123077600-123128200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:123081000-123116000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:123085800-123120800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:123086400-123115000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:123086400-123115000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:123086400-123116400	Strong transcription	Fetal Thymus	thymus
21	chr12:123087000-123116200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:123087400-123115000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:123088000-123122200	Weak transcription	HSMMtube	muscle
24	chr12:123089000-123115400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:123096400-123113600	Weak transcription	Gastric	stomach
26	chr12:123096400-123119400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:123096400-123120200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:123097800-123122200	Weak transcription	Brain Substantia Nigra	brain
29	chr12:123099200-123122200	Weak transcription	Adipose Nuclei	Adipose
30	chr12:123099400-123116800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:123099400-123120200	Weak transcription	Fetal Brain Male	brain
32	chr12:123101600-123131000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:123104400-123114400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr12:123105600-123121200	Weak transcription	Left Ventricle	heart
35	chr12:123105800-123113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:123105800-123122200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:123105800-123122400	Weak transcription	NH-A	brain
38	chr12:123105800-123124600	Weak transcription	Fetal Brain Female	brain
39	chr12:123106000-123119000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:123106200-123121400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:123106800-123113200	Weak transcription	Liver	Liver
42	chr12:123106800-123113400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:123106800-123120600	Weak transcription	Brain Germinal Matrix	brain
44	chr12:123107000-123122200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:123107800-123122200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:123108000-123116400	Weak transcription	Fetal Kidney	kidney
47	chr12:123108000-123119800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:123108000-123131400	Weak transcription	NHLF	lung
49	chr12:123108200-123121200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:123108200-123124200	Weak transcription	HMEC	breast

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