Variant report

Variant	rs12660341
Chromosome Location	chr6:13231980-13231981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1014820	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963839	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11966270	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967582	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11968818	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11969387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525681	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525892	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525906	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12527422	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528966	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661071	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665408	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12665414	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665416	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1569418	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16873855	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1736501	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1736502	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs175729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937765	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202024	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202026	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202055	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202056	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202057	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs202059	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202065	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs202075	0.88[EUR][1000 genomes]
rs202076	0.86[EUR][1000 genomes]
rs202078	0.82[EUR][1000 genomes]
rs2142568	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34275015	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34373947	1.00[ASN][1000 genomes]
rs364419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377019	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413167	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs426518	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs429919	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs429935	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs430216	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs434703	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs436268	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs443150	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4711946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711948	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711949	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711956	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715154	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715157	1.00[GIH][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715158	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715159	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715168	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715174	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4715183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533512	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs534266	0.86[ASN][1000 genomes]
rs534449	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs555496	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58474010	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59566077	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs602976	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355358	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355362	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73355368	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759256	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs7763251	0.89[ASN][1000 genomes]
rs7765972	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432849	chr6:13225077-13253733	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2535563	chr6:13230449-13231990	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12660341	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13208200-13239800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:13217800-13242400	Weak transcription	Pancreas	Pancrea
3	chr6:13218200-13235000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:13218400-13241000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:13218600-13234400	Weak transcription	HSMM	muscle
6	chr6:13223200-13232200	Weak transcription	Lung	lung
7	chr6:13227400-13232400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:13227800-13233200	Strong transcription	Left Ventricle	heart
9	chr6:13227800-13235600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13227800-13238600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:13228000-13236000	Weak transcription	Fetal Brain Male	brain
14	chr6:13228400-13232800	Strong transcription	Brain Germinal Matrix	brain
15	chr6:13228400-13237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
17	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:13229600-13233200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:13229600-13233200	Strong transcription	Aorta	Aorta
20	chr6:13230000-13232800	Strong transcription	Fetal Brain Female	brain
21	chr6:13230000-13233200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:13230000-13233200	Strong transcription	Brain Angular Gyrus	brain
23	chr6:13230000-13233400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:13230000-13236000	Strong transcription	Brain Anterior Caudate	brain
25	chr6:13230000-13239800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:13230200-13232800	Strong transcription	Brain Cingulate Gyrus	brain
27	chr6:13230200-13232800	Strong transcription	Brain Hippocampus Middle	brain
28	chr6:13230200-13234200	Weak transcription	Liver	Liver
29	chr6:13230200-13235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:13230200-13242400	Weak transcription	Fetal Intestine Small	intestine
31	chr6:13230600-13232400	Weak transcription	Right Ventricle	heart
32	chr6:13230600-13233200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:13230600-13234200	Weak transcription	NHDF-Ad	bronchial
34	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
35	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:13231000-13234000	Weak transcription	HSMMtube	muscle
37	chr6:13231200-13232000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:13231200-13232000	Weak transcription	GM12878-XiMat	blood
39	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
40	chr6:13231600-13232000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:13231800-13233000	Strong transcription	Fetal Heart	heart
42	chr6:13231800-13233600	Strong transcription	Primary hematopoietic stem cells	blood

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