Variant report

Variant	rs202067
Chromosome Location	chr6:13266065-13266066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:
2	chr6:13265469..13267865-chr6:13268622..13270348,2	K562	blood:
3	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10948561	0.91[EUR][1000 genomes]
rs12527600	0.92[EUR][1000 genomes]
rs12529141	0.92[EUR][1000 genomes]
rs1569418	0.82[JPT][hapmap]
rs16873893	0.87[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1706941	0.85[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs1736502	1.00[CHD][hapmap];0.80[MEX][hapmap]
rs17667989	0.88[AMR][1000 genomes]
rs202024	1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs202026	0.82[JPT][hapmap]
rs202031	0.88[AMR][1000 genomes]
rs202033	0.88[AMR][1000 genomes]
rs202037	1.00[ASW][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs202043	0.85[AMR][1000 genomes]
rs202049	0.85[AMR][1000 genomes]
rs202052	0.85[AMR][1000 genomes]
rs202055	1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs202058	0.80[EUR][1000 genomes]
rs202059	0.82[JPT][hapmap]
rs202065	0.83[CHD][hapmap];0.81[MEX][hapmap]
rs202076	0.85[AMR][1000 genomes]
rs202078	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34373947	0.86[EUR][1000 genomes]
rs364493	1.00[MKK][hapmap]
rs366332	0.87[CEU][hapmap]
rs369946	0.88[AMR][1000 genomes]
rs393032	0.85[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs396360	0.87[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.92[EUR][1000 genomes]
rs408284	0.86[CEU][hapmap]
rs416852	0.87[CEU][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs417024	1.00[ASW][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs426518	0.87[CEU][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.91[EUR][1000 genomes]
rs428975	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs430216	1.00[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap]
rs434923	0.88[AMR][1000 genomes]
rs435466	0.87[CEU][hapmap]
rs436268	1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs436490	0.89[EUR][1000 genomes]
rs449321	0.87[CEU][hapmap]
rs45450	0.85[CEU][hapmap]
rs4711945	0.86[EUR][1000 genomes]
rs4711948	0.82[JPT][hapmap]
rs4711949	0.82[JPT][hapmap]
rs4711956	0.82[JPT][hapmap]
rs4715168	0.82[JPT][hapmap]
rs521960	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs527857	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs534266	0.91[EUR][1000 genomes]
rs534404	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs534449	1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs546673	0.87[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.92[EUR][1000 genomes]
rs595864	0.87[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs644309	0.88[AMR][1000 genomes]
rs7759256	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs7763251	0.91[EUR][1000 genomes]
rs7765972	0.84[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv2761063	chr6:13265334-13268211	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202067	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:13248800-13266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
5	chr6:13256400-13266400	Weak transcription	Aorta	Aorta
6	chr6:13256600-13267000	Weak transcription	Fetal Stomach	stomach
7	chr6:13256600-13268800	Weak transcription	Right Ventricle	heart
8	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
11	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
12	chr6:13259400-13267400	Weak transcription	Fetal Heart	heart
13	chr6:13259800-13266800	Weak transcription	K562	blood
14	chr6:13260600-13266600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:13261000-13266600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:13261000-13268800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:13261400-13266400	Weak transcription	Lung	lung
18	chr6:13261400-13272200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:13261400-13272200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:13261400-13273000	Weak transcription	Adipose Nuclei	Adipose
21	chr6:13261600-13272200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:13262600-13272400	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:13262600-13272800	Weak transcription	Primary T cells from cord blood	blood
24	chr6:13263000-13266400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:13263200-13269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:13263400-13266200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:13263400-13266400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:13263400-13268800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:13263400-13272400	Weak transcription	Spleen	Spleen
30	chr6:13263600-13266600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:13263800-13266800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:13263800-13267800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr6:13264000-13266200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:13264200-13266400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:13264200-13267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:13264600-13272200	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:13265400-13267800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:13265800-13267200	Weak transcription	Primary B cells from cord blood	blood
39	chr6:13265800-13267800	Strong transcription	Brain Anterior Caudate	brain
40	chr6:13266000-13267400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:13266000-13267400	Strong transcription	Fetal Brain Female	brain

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