Variant report

Variant	rs7759256
Chromosome Location	chr6:13229654-13229655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13229428..13229988-chr6:13331125..13332279,5	K562	blood:
2	chr6:13229038..13230199-chr6:13278152..13279105,5	MCF-7	breast:
3	chr6:13227632..13230364-chr6:13328169..13330361,2	MCF-7	breast:
4	chr6:13229176..13229828-chr6:13332068..13332698,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112137	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1014820	0.83[ASN][1000 genomes]
rs10948550	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs10948561	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11751747	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs11755185	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs11963839	1.00[ASN][1000 genomes]
rs11966270	0.88[ASN][1000 genomes]
rs11967582	0.94[ASN][1000 genomes]
rs11968818	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11969387	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs12525681	0.88[ASN][1000 genomes]
rs12527422	0.88[ASN][1000 genomes]
rs12527600	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12527775	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs12528951	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs12528966	0.88[ASN][1000 genomes]
rs12529141	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12660341	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs12660392	0.92[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs12660606	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs12661071	0.86[ASN][1000 genomes]
rs12665414	0.81[ASN][1000 genomes]
rs12665416	0.81[ASN][1000 genomes]
rs1569418	0.85[JPT][hapmap]
rs16873855	0.92[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs16873893	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1706941	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs175729	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs202024	0.85[JPT][hapmap]
rs202026	0.85[JPT][hapmap]
rs202055	0.85[JPT][hapmap]
rs202058	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs202059	0.85[JPT][hapmap]
rs202061	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs202062	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs202063	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs202067	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2142568	1.00[ASN][1000 genomes]
rs34275015	0.88[ASN][1000 genomes]
rs34373947	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs364419	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs377019	0.88[ASN][1000 genomes]
rs393032	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs396360	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs416852	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426518	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs428975	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs430216	0.85[JPT][hapmap]
rs435466	0.82[MEX][hapmap]
rs436268	0.85[JPT][hapmap]
rs436490	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711945	0.92[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711946	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs4711948	0.85[JPT][hapmap]
rs4711949	0.85[JPT][hapmap]
rs4711956	0.85[JPT][hapmap]
rs4715154	0.83[ASN][1000 genomes]
rs4715155	0.83[ASN][1000 genomes]
rs4715157	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4715158	0.83[ASN][1000 genomes]
rs4715159	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4715168	0.85[JPT][hapmap];0.82[MEX][hapmap]
rs4715174	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs4715183	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs4715184	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs521960	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs527857	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs534266	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs534404	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs534449	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs546673	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59566077	0.83[ASN][1000 genomes]
rs595864	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs602976	0.88[ASN][1000 genomes]
rs603394	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs73355358	0.88[ASN][1000 genomes]
rs73355362	0.87[ASN][1000 genomes]
rs73355368	0.88[ASN][1000 genomes]
rs7763251	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7765972	0.85[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7759256	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13182000-13230000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:13203200-13230200	Weak transcription	Fetal Stomach	stomach
3	chr6:13206400-13229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:13206400-13230000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:13208200-13239800	Weak transcription	Brain Substantia Nigra	brain
6	chr6:13208400-13230200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:13212400-13229800	Weak transcription	Right Ventricle	heart
8	chr6:13213400-13230000	Weak transcription	Fetal Brain Female	brain
9	chr6:13217800-13230000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:13217800-13230000	Weak transcription	Spleen	Spleen
11	chr6:13217800-13242400	Weak transcription	Pancreas	Pancrea
12	chr6:13218200-13230200	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:13218200-13235000	Weak transcription	Adipose Nuclei	Adipose
14	chr6:13218400-13241000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:13218600-13230000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:13218600-13234400	Weak transcription	HSMM	muscle
17	chr6:13218800-13229800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:13218800-13230200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:13219000-13230000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:13221400-13230000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:13223200-13232200	Weak transcription	Lung	lung
22	chr6:13224600-13231800	Weak transcription	Fetal Heart	heart
23	chr6:13227400-13232400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:13227800-13233200	Strong transcription	Left Ventricle	heart
25	chr6:13227800-13235600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:13227800-13238600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:13228000-13236000	Weak transcription	Fetal Brain Male	brain
30	chr6:13228200-13229800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr6:13228200-13230200	Enhancers	Primary T cells from cord blood	blood
32	chr6:13228200-13230200	Enhancers	Fetal Intestine Large	intestine
33	chr6:13228200-13230200	Enhancers	Fetal Intestine Small	intestine
34	chr6:13228400-13232800	Strong transcription	Brain Germinal Matrix	brain
35	chr6:13228400-13237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:13228600-13231000	Enhancers	Primary B cells from cord blood	blood
37	chr6:13228800-13230400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr6:13228800-13230400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr6:13228800-13230600	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr6:13228800-13231200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:13229000-13230400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:13229000-13230600	Flanking Active TSS	GM12878-XiMat	blood
43	chr6:13229200-13229800	Enhancers	Placenta	Placenta
44	chr6:13229200-13230400	Enhancers	Fetal Thymus	thymus
45	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
46	chr6:13229400-13230000	Enhancers	Fetal Muscle Trunk	muscle
47	chr6:13229400-13230200	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:13229400-13230200	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr6:13229400-13230400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:13229400-13230400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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