Variant report

Variant	rs2496141
Chromosome Location	chr6:13311652-13311653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13310952..13313118-chr6:13315206..13317513,2	K562	blood:
2	chr6:13310969..13313189-chr6:13327909..13329582,2	K562	blood:
3	chr6:13309961..13312090-chr6:13332724..13334701,2	K562	blood:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12203576	0.82[JPT][hapmap]
rs1899262	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202020	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439538	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439546	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2496143	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496155	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs364884	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs381134	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs398151	0.80[ASN][1000 genomes]
rs408639	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs408923	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs446843	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs546520	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs570338	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs629262	0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs629728	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs641293	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs641688	0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774863	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878698	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381915	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2496141	PHACTR1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
3	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:13298200-13326800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:13299600-13326600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:13299800-13326400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:13300200-13311800	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:13300200-13327000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:13301200-13325400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:13303400-13315200	Weak transcription	Small Intestine	intestine
14	chr6:13303400-13315800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:13303800-13315800	Weak transcription	HMEC	breast
16	chr6:13303800-13327800	Weak transcription	Stomach Mucosa	stomach
17	chr6:13304200-13312000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:13304200-13315000	Weak transcription	Hela-S3	cervix
19	chr6:13304200-13315200	Weak transcription	Aorta	Aorta
20	chr6:13304400-13316800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:13304400-13327800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:13304600-13325600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:13304600-13326200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:13304800-13315200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:13304800-13315800	Weak transcription	Colonic Mucosa	Colon
26	chr6:13304800-13315800	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:13305200-13316400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:13305200-13325800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr6:13305400-13315800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:13305400-13315800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:13305400-13326200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:13305600-13313800	Weak transcription	HSMMtube	muscle
33	chr6:13305600-13315200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:13305800-13313800	Weak transcription	Brain Anterior Caudate	brain
35	chr6:13305800-13313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:13305800-13314800	Weak transcription	Esophagus	oesophagus
37	chr6:13305800-13315000	Weak transcription	NHLF	lung
38	chr6:13305800-13315200	Weak transcription	Lung	lung
39	chr6:13305800-13315200	Weak transcription	Pancreas	Pancrea
40	chr6:13305800-13315400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:13305800-13315800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:13305800-13316000	Weak transcription	Brain Angular Gyrus	brain
43	chr6:13305800-13319000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:13305800-13326200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:13306200-13313400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:13306400-13314400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:13307000-13312000	Strong transcription	NH-A	brain
48	chr6:13307200-13326200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr6:13307400-13326400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:13307800-13314400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links