Variant report

Variant	rs2952291
Chromosome Location	chr17:66460984-66460985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66459711..66462388-chr17:66755593..66757807,2	K562	blood:
2	chr17:66459308..66461889-chr17:66462514..66465217,2	K562	blood:
3	chr17:66458968..66465648-chr17:66506510..66510180,10	MCF-7	breast:
4	chr17:66243680..66245835-chr17:66460969..66462879,2	MCF-7	breast:
5	chr17:66460499..66464491-chr17:66506500..66510531,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265100	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000196704	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1030098	1.00[CHB][hapmap]
rs11656906	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12453629	1.00[CHB][hapmap]
rs12943181	0.87[ASW][hapmap]
rs1808333	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2287301	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs2302782	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2909212	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2909214	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2952278	1.00[ASW][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs2952282	0.80[AFR][1000 genomes]
rs6501512	1.00[CHB][hapmap]
rs71378929	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7207491	1.00[CHB][hapmap]
rs7222188	1.00[CHB][hapmap]
rs8066131	1.00[CHB][hapmap]
rs8069982	1.00[CHB][hapmap]
rs869657	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs918167	1.00[ASW][hapmap];0.84[GIH][hapmap];1.00[YRI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2952291	WIPI1	cis	parietal	SCAN
rs2952291	CD79B	cis	cerebellum	SCAN
rs2952291	PITPNC1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66453600-66462000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:66454600-66464000	Weak transcription	Aorta	Aorta
3	chr17:66454600-66465200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:66454600-66470400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:66454800-66462000	Weak transcription	Small Intestine	intestine
6	chr17:66454800-66462200	Weak transcription	Placenta	Placenta
7	chr17:66454800-66463600	Weak transcription	Right Atrium	heart
8	chr17:66456800-66470400	Weak transcription	Right Ventricle	heart
9	chr17:66457800-66462000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:66458000-66462000	Weak transcription	Left Ventricle	heart
11	chr17:66459000-66461000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr17:66459200-66461400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:66459200-66461400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr17:66459200-66461600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:66459200-66461800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:66459200-66461800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr17:66459200-66461800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:66459200-66462000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr17:66459200-66462000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:66459200-66462000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:66459200-66462000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:66459200-66462000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr17:66459200-66462000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr17:66459200-66462000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr17:66459200-66462000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:66459200-66462000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr17:66459200-66462000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:66459200-66462000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:66459200-66462000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:66459200-66462000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:66459200-66462000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:66459200-66462000	Weak transcription	Adipose Nuclei	Adipose
33	chr17:66459200-66462000	Weak transcription	Brain Anterior Caudate	brain
34	chr17:66459200-66462000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:66459200-66462000	Weak transcription	Brain Hippocampus Middle	brain
36	chr17:66459200-66462000	Weak transcription	Esophagus	oesophagus
37	chr17:66459200-66462000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr17:66459200-66462000	Weak transcription	Hela-S3	cervix
39	chr17:66459200-66462000	Weak transcription	HMEC	breast
40	chr17:66459200-66462000	Weak transcription	NHDF-Ad	bronchial
41	chr17:66459200-66462000	Weak transcription	NHLF	lung
42	chr17:66459200-66462200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr17:66459200-66463000	Weak transcription	HSMMtube	muscle
44	chr17:66459200-66464000	Weak transcription	HSMM	muscle
45	chr17:66459200-66466200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:66459400-66461800	Weak transcription	Dnd41	blood
47	chr17:66459400-66462000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr17:66459400-66462000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:66459400-66462000	Weak transcription	Fetal Thymus	thymus
50	chr17:66459400-66462000	Weak transcription	GM12878-XiMat	blood

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