Variant report

Variant	rs12692412
Chromosome Location	chr2:10720054-10720055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10719698..10722535-chr2:10800547..10802528,2	MCF-7	breast:
2	chr2:10719200..10721261-chr2:10727645..10731162,3	K562	blood:
3	chr2:10719236..10721261-chr2:10727853..10731162,3	K562	blood:
4	chr2:10586791..10588467-chr2:10719063..10720945,2	K562	blood:
5	chr2:10719786..10721769-chr2:10722160..10724632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115758	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000234818	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10084172	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs10166765	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167779	0.82[ASN][1000 genomes]
rs10168351	0.91[ASN][1000 genomes]
rs10168852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10174605	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10175884	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10177062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10178751	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10179854	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10182589	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183359	0.91[ASN][1000 genomes]
rs10183883	0.86[ASN][1000 genomes]
rs10186984	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs10187659	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10188373	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10190673	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10190774	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10198971	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199635	0.89[ASN][1000 genomes]
rs10199831	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202370	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10207885	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs10208103	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211190	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803724	0.90[ASN][1000 genomes]
rs10803725	0.90[ASN][1000 genomes]
rs10929677	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929678	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929679	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929680	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929681	0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929683	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs10929684	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs10929685	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs11680664	0.91[ASN][1000 genomes]
rs11684537	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs12104950	0.91[ASN][1000 genomes]
rs12329184	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12473787	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12473957	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474625	0.83[JPT][hapmap]
rs12476554	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs12613769	0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12618726	0.91[ASN][1000 genomes]
rs12621977	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622053	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690510	0.84[ASN][1000 genomes]
rs12692411	0.81[AFR][1000 genomes]
rs12692414	0.87[ASN][1000 genomes]
rs12692420	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12995465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12996735	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13009015	0.90[ASN][1000 genomes]
rs13027316	0.82[ASN][1000 genomes]
rs13407040	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs13424648	0.89[ASN][1000 genomes]
rs13425171	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13427815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13430911	0.90[ASN][1000 genomes]
rs1861299	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs1861300	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2024432	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs2024433	0.91[ASN][1000 genomes]
rs2160258	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357649	0.81[JPT][hapmap]
rs2357650	0.81[JPT][hapmap]
rs2884232	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34595606	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35859525	0.82[ASN][1000 genomes]
rs55750243	0.91[ASN][1000 genomes]
rs62127189	0.90[ASN][1000 genomes]
rs62128635	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711473	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714787	0.91[ASN][1000 genomes]
rs6717431	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720112	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721857	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722126	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730247	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732429	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs6740245	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6751436	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755281	0.90[ASN][1000 genomes]
rs744809	0.92[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap]
rs7572489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7589694	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598541	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287718	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287721	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap]
rs9973374	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9973456	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv833370	chr2:10625149-10785402	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1009897	chr2:10627248-10751468	Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12692412	PDIA6	cis	cerebellum	SCAN
rs12692412	NOL10	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10698600-10736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:10705800-10736000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr2:10707400-10728800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:10708600-10727000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:10708600-10732000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:10708800-10720600	Strong transcription	Fetal Intestine Large	intestine
7	chr2:10708800-10732800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:10709000-10725800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:10709000-10726600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:10709200-10746800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:10709400-10732600	Strong transcription	Primary B cells from cord blood	blood
12	chr2:10710400-10720200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:10710800-10721800	Weak transcription	Fetal Heart	heart
14	chr2:10712600-10720200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:10712600-10742000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:10713200-10727800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:10713800-10725600	Strong transcription	K562	blood
18	chr2:10716800-10720200	Strong transcription	A549	lung
19	chr2:10716800-10724400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:10717000-10728800	Weak transcription	Colonic Mucosa	Colon
21	chr2:10717600-10721200	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:10717600-10723800	Weak transcription	NHDF-Ad	bronchial
23	chr2:10717600-10724000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:10717600-10724200	Weak transcription	Right Ventricle	heart
25	chr2:10717600-10725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:10717600-10732400	Weak transcription	Fetal Brain Male	brain
27	chr2:10717800-10720200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:10717800-10720200	Weak transcription	Fetal Intestine Small	intestine
29	chr2:10717800-10721200	Weak transcription	Brain Angular Gyrus	brain
30	chr2:10717800-10721200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:10717800-10721400	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:10717800-10721400	Weak transcription	Fetal Stomach	stomach
33	chr2:10717800-10721400	Weak transcription	Lung	lung
34	chr2:10717800-10721400	Weak transcription	Spleen	Spleen
35	chr2:10717800-10722400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:10717800-10722400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:10717800-10722600	Weak transcription	Gastric	stomach
38	chr2:10717800-10722800	Weak transcription	Esophagus	oesophagus
39	chr2:10717800-10724000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:10717800-10724000	Weak transcription	Ovary	ovary
41	chr2:10717800-10725400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:10717800-10725400	Weak transcription	NHLF	lung
43	chr2:10717800-10726000	Weak transcription	Brain Germinal Matrix	brain
44	chr2:10717800-10726400	Weak transcription	HUVEC	blood vessel
45	chr2:10717800-10727600	Weak transcription	Brain Anterior Caudate	brain
46	chr2:10717800-10729000	Weak transcription	Small Intestine	intestine
47	chr2:10718000-10720200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:10718000-10721400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:10718000-10721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:10718000-10721600	Weak transcription	Aorta	Aorta

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