Variant report

Variant	rs12205644
Chromosome Location	chr6:13223996-13223997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13223124..13224851-chr6:13327319..13330262,2	MCF-7	breast:
2	chr6:13211847..13215247-chr6:13222867..13225283,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D7-3	chr6:13223821-13224210	NONHSAT107794

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction
ENSG00000206702	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1008462	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1014608	0.85[CEU][hapmap]
rs10948546	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13211846	0.85[CEU][hapmap]
rs2840336	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs371122	0.81[AMR][1000 genomes]
rs4711939	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715156	0.90[ASN][1000 genomes]
rs4715166	0.82[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4715167	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715169	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6458720	0.88[CEU][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928740	0.88[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7749528	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9942440	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12205644	PHACTR1	cis	Whole Blood	GTEx
rs12205644	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13182000-13230000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:13203200-13230200	Weak transcription	Fetal Stomach	stomach
3	chr6:13206400-13229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:13206400-13230000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:13208200-13239800	Weak transcription	Brain Substantia Nigra	brain
6	chr6:13208400-13230200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:13212400-13229800	Weak transcription	Right Ventricle	heart
8	chr6:13213400-13230000	Weak transcription	Fetal Brain Female	brain
9	chr6:13214000-13227400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:13217800-13230000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:13217800-13230000	Weak transcription	Spleen	Spleen
12	chr6:13217800-13242400	Weak transcription	Pancreas	Pancrea
13	chr6:13218200-13227800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:13218200-13230200	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:13218200-13235000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:13218400-13241000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:13218600-13227800	Weak transcription	Left Ventricle	heart
18	chr6:13218600-13230000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:13218600-13234400	Weak transcription	HSMM	muscle
20	chr6:13218800-13228200	Weak transcription	Fetal Intestine Small	intestine
21	chr6:13218800-13229800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:13218800-13230200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:13219000-13230000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:13219800-13229600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:13220400-13228400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:13221000-13225000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:13221400-13228400	Weak transcription	Brain Germinal Matrix	brain
28	chr6:13221400-13230000	Weak transcription	Brain Anterior Caudate	brain
29	chr6:13222400-13224800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:13223000-13225000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:13223200-13224200	Weak transcription	Aorta	Aorta
32	chr6:13223200-13232200	Weak transcription	Lung	lung
33	chr6:13223800-13224600	Strong transcription	Fetal Heart	heart

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