Variant report

Variant	rs7309390
Chromosome Location	chr12:123110422-123110423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10734924	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744211	0.88[JPT][hapmap]
rs10744275	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10744287	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10773208	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10773302	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773394	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10846921	1.00[JPT][hapmap]
rs10846978	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10847179	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10847242	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10847415	0.81[CEU][hapmap]
rs10998	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs11058226	1.00[JPT][hapmap]
rs11058402	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1392236	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1473553	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1973463	0.88[JPT][hapmap]
rs2062506	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2173628	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2342082	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3803005	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319547	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758643	0.88[JPT][hapmap]
rs61954972	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61954973	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6489071	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6489156	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489157	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489158	0.97[ASN][1000 genomes]
rs6489159	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7295105	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7295397	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7307233	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7307735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314638	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7316149	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7316734	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7397990	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954006	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs7955203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959238	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7964138	1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7966094	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972728	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9705654	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9988963	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[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:108 , 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	chr12:123013200-123112400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:123013400-123120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:123015600-123115000	Strong transcription	Dnd41	blood
7	chr12:123022600-123113800	Weak transcription	Colonic Mucosa	Colon
8	chr12:123037200-123113000	Weak transcription	Brain Anterior Caudate	brain
9	chr12:123038400-123120000	Weak transcription	Small Intestine	intestine
10	chr12:123043800-123121800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:123050800-123112600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:123050800-123115200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:123059400-123119000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:123060200-123113000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:123077400-123137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:123077600-123115000	Weak transcription	Esophagus	oesophagus
17	chr12:123077600-123128200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:123081000-123116000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:123084600-123112600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:123085800-123120800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:123086200-123112200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:123086400-123111800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:123086400-123115000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:123086400-123115000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:123086400-123116400	Strong transcription	Fetal Thymus	thymus
26	chr12:123087000-123116200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:123087400-123115000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:123088000-123122200	Weak transcription	HSMMtube	muscle
29	chr12:123089000-123115400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:123096400-123112000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:123096400-123113600	Weak transcription	Gastric	stomach
32	chr12:123096400-123119400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:123096400-123120200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:123097800-123112200	Strong transcription	GM12878-XiMat	blood
35	chr12:123097800-123122200	Weak transcription	Brain Substantia Nigra	brain
36	chr12:123098000-123111800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:123099200-123111200	Weak transcription	Spleen	Spleen
38	chr12:123099200-123122200	Weak transcription	Adipose Nuclei	Adipose
39	chr12:123099400-123112800	Weak transcription	Lung	lung
40	chr12:123099400-123116800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:123099400-123120200	Weak transcription	Fetal Brain Male	brain
42	chr12:123101600-123131000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:123104200-123112400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:123104400-123114400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:123104800-123110600	Strong transcription	Osteobl	bone
46	chr12:123104800-123112200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:123104800-123112200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:123105600-123111200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:123105600-123121200	Weak transcription	Left Ventricle	heart
50	chr12:123105800-123111200	Weak transcription	Rectal Mucosa Donor 29	rectum

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