Variant report

Variant	rs202033
Chromosome Location	chr6:13291523-13291524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13291471-13291881	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:13284835-13292200	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:13291450-13292003	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
2	chr6:13290208..13292111-chr6:13295404..13298068,2	K562	blood:

Variant related genes	Relation type
ENSG00000272379	TF binding region
ENSG00000215022	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12525892	0.89[AMR][1000 genomes]
rs12525906	0.89[AMR][1000 genomes]
rs12665408	0.86[AMR][1000 genomes]
rs1736501	0.89[AMR][1000 genomes]
rs1736502	0.89[AMR][1000 genomes]
rs17667989	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937765	0.84[AMR][1000 genomes]
rs202024	0.89[AMR][1000 genomes]
rs202026	0.89[AMR][1000 genomes]
rs202031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202037	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202043	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs202049	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs202052	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202055	0.89[AMR][1000 genomes]
rs202056	0.87[AMR][1000 genomes]
rs202059	0.86[AMR][1000 genomes]
rs202065	0.80[AMR][1000 genomes]
rs202067	0.88[AMR][1000 genomes]
rs202075	0.87[AMR][1000 genomes]
rs202076	0.97[AMR][1000 genomes]
rs202078	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs369946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413167	0.89[AMR][1000 genomes]
rs417024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429919	0.89[AMR][1000 genomes]
rs429935	0.89[AMR][1000 genomes]
rs430216	0.89[AMR][1000 genomes]
rs434703	0.89[AMR][1000 genomes]
rs434923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436268	0.89[AMR][1000 genomes]
rs443150	0.89[AMR][1000 genomes]
rs4711948	0.89[AMR][1000 genomes]
rs4711949	0.89[AMR][1000 genomes]
rs4711956	0.89[AMR][1000 genomes]
rs533512	0.89[AMR][1000 genomes]
rs534449	0.87[AMR][1000 genomes]
rs555496	0.89[AMR][1000 genomes]
rs644309	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349559	1.00[ASN][1000 genomes]
rs9367421	1.00[ASN][1000 genomes]
rs9369989	1.00[ASN][1000 genomes]
rs9381897	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202033	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13270200-13291600	Weak transcription	HSMM	muscle
2	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
3	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:13280000-13292600	Weak transcription	NHLF	lung
6	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
11	chr6:13285800-13293000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:13285800-13293000	Weak transcription	Brain Substantia Nigra	brain
13	chr6:13286600-13291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:13286600-13292800	Weak transcription	Colonic Mucosa	Colon
15	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:13287200-13292000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:13287200-13292800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
19	chr6:13287800-13291800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:13287800-13294200	Weak transcription	A549	lung
21	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:13288000-13292200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:13288000-13294600	Weak transcription	Fetal Brain Male	brain
25	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr6:13288200-13291600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:13288200-13291600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:13288200-13291600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:13288200-13291600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:13288200-13291600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:13288200-13291600	Weak transcription	Brain Germinal Matrix	brain
32	chr6:13288200-13291600	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:13288200-13291600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:13288200-13292600	Weak transcription	Placenta	Placenta
35	chr6:13288200-13294200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:13288200-13294200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:13288200-13295400	Weak transcription	Fetal Heart	heart
38	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
39	chr6:13288400-13291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:13288400-13293200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:13288400-13294200	Weak transcription	Osteobl	bone
42	chr6:13288400-13294800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
44	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:13288600-13291600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:13288600-13292400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr6:13288600-13293800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:13288600-13294200	Weak transcription	Esophagus	oesophagus
49	chr6:13288600-13295000	Strong transcription	Primary B cells from cord blood	blood
50	chr6:13288600-13295000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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