Variant report

Variant	rs2458310
Chromosome Location	chr6:13310308-13310309
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13305462..13308296-chr6:13309650..13311339,2	K562	blood:
2	chr6:13309961..13312090-chr6:13332724..13334701,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1223397	0.81[JPT][hapmap]
rs13203254	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs202016	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202017	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202021	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]
rs202022	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20499	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs20500	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439535	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439540	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439543	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439544	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439549	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458300	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458309	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2458314	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496149	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496151	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496152	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496153	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496154	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496157	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2919685	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919686	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001966	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001967	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001968	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs364493	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3817737	0.80[ASN][1000 genomes]
rs3817738	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817741	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817742	0.80[ASN][1000 genomes]
rs402705	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452309	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453877	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488297	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59639740	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617580	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs641758	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]
rs9349564	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381884	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9395602	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs957175	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957176	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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
rs2458310	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL
rs2458310	RP1-257A7.4	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	chr6:13290400-13310400	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	chr6:13298200-13326800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13299600-13326600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:13299800-13326400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:13300200-13311800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:13300200-13327000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:13301200-13325400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:13303400-13315200	Weak transcription	Small Intestine	intestine
16	chr6:13303400-13315800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:13303800-13315800	Weak transcription	HMEC	breast
18	chr6:13303800-13327800	Weak transcription	Stomach Mucosa	stomach
19	chr6:13304200-13312000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:13304200-13315000	Weak transcription	Hela-S3	cervix
21	chr6:13304200-13315200	Weak transcription	Aorta	Aorta
22	chr6:13304400-13316800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:13304400-13327800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:13304600-13325600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:13304600-13326200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:13304800-13315200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:13304800-13315800	Weak transcription	Colonic Mucosa	Colon
28	chr6:13304800-13315800	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:13305000-13310400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr6:13305200-13316400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr6:13305200-13325800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr6:13305400-13310400	Strong transcription	Fetal Brain Female	brain
33	chr6:13305400-13315800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:13305400-13315800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:13305400-13326200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:13305600-13311400	Weak transcription	Fetal Brain Male	brain
37	chr6:13305600-13313800	Weak transcription	HSMMtube	muscle
38	chr6:13305600-13315200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:13305800-13313800	Weak transcription	Brain Anterior Caudate	brain
40	chr6:13305800-13313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:13305800-13314800	Weak transcription	Esophagus	oesophagus
42	chr6:13305800-13315000	Weak transcription	NHLF	lung
43	chr6:13305800-13315200	Weak transcription	Lung	lung
44	chr6:13305800-13315200	Weak transcription	Pancreas	Pancrea
45	chr6:13305800-13315400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:13305800-13315800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:13305800-13316000	Weak transcription	Brain Angular Gyrus	brain
48	chr6:13305800-13319000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:13305800-13326200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:13306200-13313400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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