Variant report

Variant	rs12738010
Chromosome Location	chr1:86102575-86102576
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1047893	0.84[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap]
rs10493773	0.88[CEU][hapmap]
rs10493774	0.88[CEU][hapmap]
rs10873716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11161645	0.81[CHD][hapmap];0.86[TSI][hapmap]
rs11161649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161650	0.87[ASN][1000 genomes]
rs11161651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11161656	0.87[ASN][1000 genomes]
rs11161659	0.86[ASN][1000 genomes]
rs11161660	0.87[ASN][1000 genomes]
rs11161662	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161664	0.87[ASN][1000 genomes]
rs12058974	0.87[ASN][1000 genomes]
rs12075929	0.96[CEU][hapmap]
rs12097932	0.87[ASN][1000 genomes]
rs12564080	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12566746	0.87[CHB][hapmap]
rs12739713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12754358	0.84[CEU][hapmap]
rs12756013	0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12757270	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12758511	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1539444	0.85[ASW][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs2069208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274738	0.88[CEU][hapmap]
rs2389970	0.82[CHD][hapmap]
rs2389972	0.87[ASN][1000 genomes]
rs35438778	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3753786	0.84[ASW][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap]
rs3753789	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs3753790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3767163	0.88[CEU][hapmap]
rs414618	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs6576784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672312	0.84[ASW][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap]
rs6689168	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs6697535	0.87[CHB][hapmap]
rs6698578	0.87[CEU][hapmap]
rs7518312	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7520491	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12738010	ZNHIT6	cis	lymphoblastoid	seeQTL
rs12738010	C1orf181	cis	multi-tissue	Pritchard
rs12738010	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs12738010	DNASE2B	cis	cerebellum	SCAN
rs12738010	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs12738010	DDAH1	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:86088400-86103000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:86088600-86103000	Weak transcription	NHEK	skin
4	chr1:86089400-86102600	Weak transcription	GM12878-XiMat	blood
5	chr1:86089400-86103000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:86091200-86103200	Weak transcription	Brain Angular Gyrus	brain
7	chr1:86091800-86107600	Weak transcription	Colonic Mucosa	Colon
8	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:86094800-86103200	Weak transcription	Small Intestine	intestine
10	chr1:86095000-86102800	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:86095000-86103200	Weak transcription	Fetal Heart	heart
12	chr1:86095200-86102600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:86095200-86102800	Weak transcription	Fetal Stomach	stomach
14	chr1:86095200-86103000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:86095200-86103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:86095200-86103000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:86095200-86103000	Weak transcription	Gastric	stomach
18	chr1:86095200-86103000	Weak transcription	Ovary	ovary
19	chr1:86095200-86103000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:86095200-86103000	Weak transcription	Spleen	Spleen
21	chr1:86095200-86104200	Weak transcription	Psoas Muscle	Psoas
22	chr1:86095200-86104400	Weak transcription	Right Ventricle	heart
23	chr1:86095400-86102600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:86095400-86102800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:86095400-86103000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:86095400-86103000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:86095400-86103000	Weak transcription	Brain Anterior Caudate	brain
28	chr1:86095400-86103000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:86095400-86107600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:86095600-86103000	Weak transcription	Fetal Lung	lung
33	chr1:86095600-86103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:86095600-86104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:86095600-86104000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:86095600-86117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:86095800-86102600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:86095800-86103000	Weak transcription	HSMMtube	muscle
39	chr1:86095800-86103200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:86096000-86103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:86096000-86104000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:86096200-86102600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:86096200-86102800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:86096200-86103400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:86096200-86103800	Weak transcription	HepG2	liver
46	chr1:86096200-86115600	Weak transcription	NH-A	brain
47	chr1:86096400-86102600	Weak transcription	A549	lung
48	chr1:86096400-86103000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:86096400-86103000	Weak transcription	NHDF-Ad	bronchial
50	chr1:86096400-86104800	Weak transcription	Muscle Satellite Cultured Cells	--

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