Variant report

Variant	rs17153204
Chromosome Location	chr10:6335731-6335732
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	chr10:6320265..6323199-chr10:6333392..6336279,3	MCF-7	breast:
2	chr10:6333704..6336118-chr10:6337786..6340640,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKCQ-4	chr10:6335615-6335908	NONHSAT011222

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17297219	0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4750246	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh 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	40 gene(s)	inside rSNPs	diseases
3	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17153204	VAMP8	trans	brain	seeQTL
rs17153204	ALOX5AP	trans	brain	seeQTL
rs17153204	TSPO	trans	brain	seeQTL
rs17153204	IL15RA	cis	parietal	SCAN
rs17153204	IL2RA	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6318000-6337600	Weak transcription	Primary B cells from cord blood	blood
2	chr10:6318200-6337800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:6322600-6337600	Weak transcription	Spleen	Spleen
4	chr10:6322600-6339000	Weak transcription	Esophagus	oesophagus
5	chr10:6332800-6335800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr10:6332800-6338800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:6333000-6335800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr10:6333000-6341800	Weak transcription	NHDF-Ad	bronchial
9	chr10:6333400-6337600	Weak transcription	Small Intestine	intestine
10	chr10:6333400-6338400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:6333400-6338600	Weak transcription	NHEK	skin
12	chr10:6333400-6338800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:6333400-6341000	Weak transcription	Thymus	Thymus
14	chr10:6333600-6337400	Weak transcription	Fetal Thymus	thymus
15	chr10:6333600-6338800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr10:6333600-6339000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:6333600-6339000	Weak transcription	Adipose Nuclei	Adipose
18	chr10:6333800-6338200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:6333800-6338600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:6333800-6338600	Weak transcription	HMEC	breast
21	chr10:6333800-6338800	Weak transcription	Stomach Mucosa	stomach
22	chr10:6333800-6339000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:6333800-6339000	Weak transcription	Brain Anterior Caudate	brain
24	chr10:6333800-6339000	Weak transcription	Fetal Lung	lung
25	chr10:6333800-6339000	Weak transcription	HepG2	liver
26	chr10:6333800-6339200	Weak transcription	Fetal Intestine Large	intestine
27	chr10:6333800-6339800	Weak transcription	Brain Substantia Nigra	brain
28	chr10:6333800-6341800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr10:6334000-6341000	Weak transcription	Dnd41	blood
30	chr10:6334000-6341600	Weak transcription	Primary T cells from cord blood	blood
31	chr10:6334000-6341600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:6334200-6339000	Weak transcription	Right Atrium	heart
33	chr10:6334200-6341200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:6334200-6341600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:6334600-6337400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr10:6334600-6337600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:6334600-6341600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:6334600-6341600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:6334800-6337200	ZNF genes & repeats	A549	lung
40	chr10:6335000-6336000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:6335000-6336600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:6335200-6338800	Weak transcription	Hela-S3	cervix
43	chr10:6335200-6339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:6335200-6339800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:6335400-6339000	Weak transcription	Fetal Kidney	kidney
46	chr10:6335600-6339800	Weak transcription	Monocytes-CD14+_RO01746	blood

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