Variant report

Variant	rs202059
Chromosome Location	chr6:13242819-13242820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13238401..13240269-chr6:13241272..13242998,2	K562	blood:
2	chr6:13241474..13243088-chr6:13272742..13274411,2	K562	blood:

Variant related genes	Relation type
ENSG00000215022	Chromatin interaction
ENSG00000112137	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1014820	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948550	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948561	0.94[ASN][1000 genomes]
rs11751747	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11755185	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11963839	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11966270	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11967582	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11968818	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11969387	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525681	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525892	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12525906	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12527422	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12527600	0.94[ASN][1000 genomes]
rs12527775	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12528951	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12528966	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12529141	0.94[ASN][1000 genomes]
rs12660341	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12660392	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12660606	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12661071	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12665408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665414	0.90[EUR][1000 genomes]
rs12665416	0.90[EUR][1000 genomes]
rs1569418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16873893	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1706941	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736501	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1736502	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs175729	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17667989	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs1937765	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202024	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202031	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs202033	0.86[AMR][1000 genomes]
rs202037	0.86[AMR][1000 genomes]
rs202043	0.89[AMR][1000 genomes]
rs202049	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs202052	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202056	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs202057	0.85[EUR][1000 genomes]
rs202061	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202062	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202063	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202065	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202067	0.82[JPT][hapmap]
rs202075	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202076	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs202078	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2142568	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34275015	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs364419	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs369946	0.86[AMR][1000 genomes]
rs377019	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs393032	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs396360	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs413167	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416852	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs417024	0.86[AMR][1000 genomes]
rs428975	0.92[ASN][1000 genomes]
rs429919	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429935	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs430216	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434703	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434923	0.86[AMR][1000 genomes]
rs436268	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs436490	0.94[ASN][1000 genomes]
rs443150	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711946	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711948	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711949	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711956	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715154	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715155	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4715157	0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs4715158	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4715159	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715168	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715174	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715183	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715184	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs521960	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs527857	0.94[ASN][1000 genomes]
rs533512	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs534404	0.94[ASN][1000 genomes]
rs534449	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546673	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs555496	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58474010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59566077	0.90[EUR][1000 genomes]
rs595864	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs602976	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs603394	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs644309	0.86[AMR][1000 genomes]
rs73355358	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73355362	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73355368	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7759256	0.85[JPT][hapmap]
rs7765972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	esv1815942	chr6:13235495-13250588	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1817130	chr6:13235495-13250588	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1830412	chr6:13235495-13250588	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1832850	chr6:13235495-13250588	Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1846185	chr6:13235495-13250588	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1848354	chr6:13235495-13250588	Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202059	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
4	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
6	chr6:13232800-13243800	Weak transcription	Fetal Brain Female	brain
7	chr6:13233200-13256000	Weak transcription	Right Ventricle	heart
8	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:13235200-13248200	Weak transcription	HSMMtube	muscle
10	chr6:13236000-13248000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:13237000-13243800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:13237600-13252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:13239000-13253200	Weak transcription	Aorta	Aorta
14	chr6:13240000-13248000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:13240200-13248000	Weak transcription	Brain Angular Gyrus	brain
16	chr6:13240200-13248000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:13240200-13248200	Weak transcription	Brain Anterior Caudate	brain
18	chr6:13240200-13251200	Weak transcription	Left Ventricle	heart
19	chr6:13240400-13248000	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:13241200-13250200	Weak transcription	Fetal Heart	heart
21	chr6:13241600-13244000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:13241600-13251200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:13242400-13243400	Enhancers	Liver	Liver
24	chr6:13242400-13243600	Enhancers	Fetal Intestine Small	intestine
25	chr6:13242600-13243000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:13242600-13243000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:13242600-13243200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:13242600-13243600	Enhancers	HepG2	liver
29	chr6:13242800-13244000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:13242800-13248200	Weak transcription	Lung	lung
31	chr6:13242800-13256000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links