Variant report

Variant	rs650652
Chromosome Location	chr10:6540723-6540724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs472317	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[ASN][1000 genomes]
rs527611	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs565660	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs620736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622998	0.89[ASN][1000 genomes]
rs634492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648778	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790816	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5687	chr10:6537209-6556751	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs650652	PRKCQ	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
2	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:6509200-6541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:6517600-6541800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr10:6518200-6556800	Weak transcription	Fetal Intestine Large	intestine
8	chr10:6519200-6544400	Weak transcription	Spleen	Spleen
9	chr10:6526600-6553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:6527400-6542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:6528400-6540800	Weak transcription	Brain Angular Gyrus	brain
12	chr10:6529000-6546200	Weak transcription	Esophagus	oesophagus
13	chr10:6529000-6552800	Weak transcription	Lung	lung
14	chr10:6530400-6552600	Weak transcription	K562	blood
15	chr10:6533800-6552800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:6534400-6545800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:6535400-6553400	Weak transcription	Gastric	stomach
18	chr10:6536000-6541400	Strong transcription	Fetal Muscle Leg	muscle
19	chr10:6536200-6540800	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr10:6536600-6552800	Weak transcription	Fetal Intestine Small	intestine
21	chr10:6536800-6540800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr10:6537200-6540800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:6537400-6552800	Weak transcription	Fetal Stomach	stomach
24	chr10:6537600-6544200	Weak transcription	Pancreas	Pancrea
25	chr10:6537600-6552600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr10:6537800-6543800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr10:6537800-6548600	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:6537800-6548800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr10:6538000-6546800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:6538200-6552800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:6539000-6540800	Enhancers	Fetal Brain Male	brain
32	chr10:6539200-6542000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr10:6539400-6541400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr10:6539600-6541800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:6539600-6542000	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr10:6539600-6542000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr10:6539600-6542200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:6539800-6540800	Enhancers	Fetal Brain Female	brain
39	chr10:6539800-6542000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr10:6539800-6542000	Genic enhancers	Dnd41	blood
41	chr10:6540000-6540800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:6540000-6541200	Enhancers	Psoas Muscle	Psoas
43	chr10:6540000-6541600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr10:6540000-6542000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr10:6540000-6542000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr10:6540200-6541200	Genic enhancers	Primary hematopoietic stem cells	blood
47	chr10:6540200-6541200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
48	chr10:6540200-6541600	Genic enhancers	Primary T cells from cord blood	blood
49	chr10:6540200-6541800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr10:6540200-6541800	Enhancers	Monocytes-CD14+_RO01746	blood

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