Variant report

Variant	rs6501512
Chromosome Location	chr17:66492736-66492737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66486234..66488484-chr17:66491556..66493277,2	MCF-7	breast:
2	chr17:66489499..66498114-chr17:66506415..66512369,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1030098	1.00[CHB][hapmap]
rs11656906	1.00[CHB][hapmap]
rs12453629	1.00[CHB][hapmap]
rs2287301	1.00[CHB][hapmap]
rs2907373	0.83[ASW][hapmap];0.86[YRI][hapmap]
rs2952278	0.89[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap]
rs2952282	0.81[ASN][1000 genomes]
rs2952291	1.00[CHB][hapmap]
rs4321253	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207491	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066131	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8069982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8076465	0.86[YRI][hapmap]
rs8080306	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs869657	1.00[CHB][hapmap]
rs9892343	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9894682	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898700	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6501512	PRKAR1A	cis	parietal	SCAN
rs6501512	CD79B	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66487200-66493800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:66488200-66493400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:66488200-66493800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:66488200-66494600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:66488400-66493800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:66488400-66494400	Weak transcription	Ovary	ovary
7	chr17:66488400-66494600	Weak transcription	Gastric	stomach
8	chr17:66488600-66493200	Weak transcription	GM12878-XiMat	blood
9	chr17:66488600-66493800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:66488600-66493800	Weak transcription	Spleen	Spleen
11	chr17:66488800-66493400	Weak transcription	Primary B cells from cord blood	blood
12	chr17:66488800-66493800	Weak transcription	Colonic Mucosa	Colon
13	chr17:66488800-66493800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr17:66488800-66494000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr17:66488800-66494200	Weak transcription	Pancreas	Pancrea
16	chr17:66489400-66494200	Weak transcription	Left Ventricle	heart
17	chr17:66489400-66494600	Weak transcription	Right Atrium	heart
18	chr17:66489600-66493800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr17:66489600-66494600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr17:66489800-66494200	Weak transcription	Fetal Muscle Leg	muscle
21	chr17:66490000-66494200	Weak transcription	Adipose Nuclei	Adipose
22	chr17:66491800-66493400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr17:66491800-66494600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr17:66492400-66494200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr17:66492600-66492800	Enhancers	Fetal Heart	heart
26	chr17:66492600-66493800	Enhancers	Primary neutrophils fromperipheralblood	blood

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