Variant report

Variant	rs2439538
Chromosome Location	chr6:13308083-13308084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13284832..13286495-chr6:13306674..13309047,2	K562	blood:
2	chr6:13206187..13208549-chr6:13306945..13308625,2	K562	blood:
3	chr6:13284063..13286332-chr6:13306674..13308343,2	K562	blood:
4	chr6:13287888..13289538-chr6:13307383..13309880,2	K562	blood:
5	chr6:13305462..13308296-chr6:13309650..13311339,2	K562	blood:
6	chr6:13307272..13309683-chr6:13313078..13314603,2	K562	blood:
7	chr6:13296819..13300441-chr6:13305761..13308537,4	K562	blood:
8	chr6:13299774..13302593-chr6:13305903..13308627,2	K562	blood:

No data

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1899262	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202020	0.91[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439546	0.95[CEU][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496141	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]
rs2496143	0.95[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2496155	0.87[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs364884	0.95[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs381134	0.95[CEU][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs398151	0.87[ASN][1000 genomes]
rs408639	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs408923	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs446843	0.95[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs546520	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs570338	0.95[CEU][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs629262	0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs629728	0.95[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs641293	0.95[CEU][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs641688	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7774863	0.95[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs860266	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs878698	0.95[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9381915	0.95[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2439538	PHACTR1	cis	Whole Blood	GTEx
rs2439538	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:127 , 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	chr6:13290400-13310400	Strong transcription	Dnd41	blood
5	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:13298000-13309600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:13298200-13326800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:13299600-13326600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:13299800-13326400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:13300200-13309200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr6:13300200-13311800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:13300200-13327000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:13301200-13325400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:13303400-13309600	Strong transcription	Fetal Thymus	thymus
18	chr6:13303400-13315200	Weak transcription	Small Intestine	intestine
19	chr6:13303400-13315800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:13303600-13308400	Weak transcription	Fetal Kidney	kidney
21	chr6:13303800-13308400	Strong transcription	Liver	Liver
22	chr6:13303800-13309800	Strong transcription	Fetal Intestine Large	intestine
23	chr6:13303800-13315800	Weak transcription	HMEC	breast
24	chr6:13303800-13327800	Weak transcription	Stomach Mucosa	stomach
25	chr6:13304200-13312000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:13304200-13315000	Weak transcription	Hela-S3	cervix
27	chr6:13304200-13315200	Weak transcription	Aorta	Aorta
28	chr6:13304400-13309600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:13304400-13316800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:13304400-13327800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:13304600-13309000	Strong transcription	HepG2	liver
32	chr6:13304600-13309200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:13304600-13325600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:13304600-13326200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:13304800-13309400	Strong transcription	Fetal Muscle Leg	muscle
36	chr6:13304800-13315200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:13304800-13315800	Weak transcription	Colonic Mucosa	Colon
38	chr6:13304800-13315800	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:13305000-13308200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:13305000-13309400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:13305000-13309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:13305000-13309600	Strong transcription	Placenta	Placenta
43	chr6:13305000-13310400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr6:13305200-13316400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:13305200-13325800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:13305400-13309400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:13305400-13309600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr6:13305400-13310400	Strong transcription	Fetal Brain Female	brain
49	chr6:13305400-13315800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:13305400-13315800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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