Variant report

Variant	rs2952270
Chromosome Location	chr17:66531149-66531150
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66530303..66532182-chr17:66536005..66538326,3	MCF-7	breast:
2	chr17:66528639..66530741-chr17:66530963..66533446,4	MCF-7	breast:
3	chr17:66530099..66531694-chr17:66754931..66757389,2	MCF-7	breast:
4	chr17:66529524..66531766-chr17:66754372..66756629,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108950	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11077609	0.87[JPT][hapmap]
rs11867767	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286557	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2302234	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2907375	0.83[ASN][1000 genomes]
rs2907387	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952272	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952273	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2952274	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952317	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56278628	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv510723	chr17:66529668-66557425	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2952270	CACNG1	cis	cerebellum	SCAN
rs2952270	PRKCA	cis	parietal	SCAN
rs2952270	PRKAR1A	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:66511800-66531600	Strong transcription	Fetal Intestine Large	intestine
4	chr17:66511800-66536600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:66511800-66537000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:66511800-66537800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:66513200-66533000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:66514800-66537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:66514800-66537400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:66514800-66537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:66515000-66535800	Strong transcription	Placenta	Placenta
12	chr17:66515200-66533400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr17:66515200-66534600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:66516600-66535800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:66516800-66535400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr17:66517200-66537600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:66517400-66537000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:66517600-66532200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:66517600-66535400	Strong transcription	HMEC	breast
20	chr17:66517600-66536800	Strong transcription	Fetal Thymus	thymus
21	chr17:66517600-66537200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:66518000-66534000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:66518000-66534600	Strong transcription	A549	lung
24	chr17:66518000-66535800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:66518000-66536800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:66518000-66537200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr17:66518200-66534600	Strong transcription	Primary B cells from cord blood	blood
28	chr17:66518200-66536600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr17:66518200-66536800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr17:66518200-66537600	Strong transcription	Primary T cells from cord blood	blood
31	chr17:66518200-66537800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr17:66518400-66532400	Strong transcription	Dnd41	blood
33	chr17:66518400-66533800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr17:66518400-66534600	Strong transcription	GM12878-XiMat	blood
35	chr17:66518400-66535600	Strong transcription	Primary hematopoietic stem cells	blood
36	chr17:66518400-66535600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr17:66518600-66532800	Strong transcription	NH-A	brain
38	chr17:66518600-66537200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:66518600-66538200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:66519000-66532000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr17:66519000-66532400	Strong transcription	HUVEC	blood vessel
42	chr17:66519000-66537200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr17:66519200-66536800	Strong transcription	Fetal Lung	lung
44	chr17:66519600-66532000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr17:66519800-66534000	Strong transcription	Fetal Kidney	kidney
46	chr17:66519800-66537800	Strong transcription	Brain Anterior Caudate	brain
47	chr17:66520400-66539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:66523200-66542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr17:66523400-66531800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:66523400-66535800	Weak transcription	Stomach Mucosa	stomach

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