Variant report

Variant	rs453877
Chromosome Location	chr6:13297463-13297464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13274083..13277421-chr6:13297082..13301885,5	K562	blood:
2	chr6:13197054..13199735-chr6:13296855..13299373,2	K562	blood:
3	chr6:13296423..13299352-chr6:13327386..13329977,2	MCF-7	breast:
4	chr6:13290208..13292111-chr6:13295404..13298068,2	K562	blood:
5	chr6:13296819..13300441-chr6:13305761..13308537,4	K562	blood:

Variant related genes	Relation type
ENSG00000215022	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000272379	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1223397	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs13191897	0.84[CHB][hapmap]
rs13203254	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17767967	0.91[CHB][hapmap]
rs202016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202018	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202021	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202022	0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202029	1.00[CHB][hapmap]
rs202032	1.00[CHB][hapmap]
rs20499	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs20500	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439534	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[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439539	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439540	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439543	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439544	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458300	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458309	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458310	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]
rs2458311	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458313	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2458314	0.80[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496140	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496147	0.80[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]
rs2496148	0.80[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]
rs2496149	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496151	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496152	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496153	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496154	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496156	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2919685	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919686	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001966	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001967	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001968	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs364493	0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3734878	0.91[CHB][hapmap]
rs3817737	0.80[ASN][1000 genomes]
rs3817738	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817741	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817742	0.80[ASN][1000 genomes]
rs402705	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59639740	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617580	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs641758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9395602	0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs957175	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957176	0.97[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
rs453877	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL
rs453877	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	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
6	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
8	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
9	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
11	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:13290200-13302800	Weak transcription	NHEK	skin
14	chr6:13290400-13310400	Strong transcription	Dnd41	blood
15	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
16	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
17	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
18	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:13291400-13297800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:13291400-13299600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:13291400-13300200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:13291600-13297600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr6:13291600-13298200	Strong transcription	Lung	lung
25	chr6:13291600-13298600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:13291600-13298600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:13291600-13300800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr6:13291600-13302400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:13291600-13302400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:13291600-13302600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:13291600-13302600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr6:13291600-13305800	Strong transcription	Thymus	Thymus
33	chr6:13291800-13301800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:13292000-13302600	Strong transcription	Fetal Intestine Large	intestine
36	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:13292400-13299800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:13292400-13302600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:13292600-13299400	Weak transcription	Psoas Muscle	Psoas
40	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:13293000-13302800	Strong transcription	Fetal Lung	lung
42	chr6:13293200-13305400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:13293800-13298800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:13294200-13302600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:13294600-13301200	Weak transcription	Brain Angular Gyrus	brain
46	chr6:13295000-13298800	Weak transcription	Aorta	Aorta
47	chr6:13295000-13300600	Weak transcription	NH-A	brain
48	chr6:13295000-13304800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:13295200-13298200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:13295200-13299000	Weak transcription	Colon Smooth Muscle	Colon

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