Variant report

Variant	rs11656906
Chromosome Location	chr17:66428893-66428894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:66428290-66428913	K562	blood:	n/a	n/a
2	CTCF	chr17:66428860-66429010	GM12875	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:66426481..66429441-chr17:66430953..66434453,4	K562	blood:
2	chr17:66285150..66290165-chr17:66423576..66430541,21	MCF-7	breast:
3	chr17:66383780..66385564-chr17:66427037..66429492,2	MCF-7	breast:
4	chr17:66286133..66290612-chr17:66424686..66436118,23	MCF-7	breast:

Variant related genes	Relation type
WIPI1	TF binding region
ENSG00000108932	Chromatin interaction
ENSG00000141337	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1030098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867297	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453629	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12940626	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12943181	0.87[ASW][hapmap]
rs1808333	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2287301	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302782	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs2361954	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909212	0.80[AFR][1000 genomes]
rs2952278	1.00[ASW][hapmap];0.93[YRI][hapmap]
rs2952291	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6501512	1.00[CHB][hapmap]
rs71378929	0.81[AFR][1000 genomes]
rs7207491	1.00[CHB][hapmap]
rs7222188	1.00[CHB][hapmap]
rs8066131	1.00[CHB][hapmap]
rs8069982	1.00[CHB][hapmap]
rs869657	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs883620	0.89[EUR][1000 genomes]
rs918167	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[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
rs11656906	WIPI1	cis	multi-tissue	Pritchard
rs11656906	PRKAR1A	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66410200-66432200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr17:66410400-66452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:66412200-66432000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr17:66414200-66432200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:66414600-66432400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:66415800-66430400	Strong transcription	HSMMtube	muscle
7	chr17:66415800-66431600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr17:66415800-66431800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr17:66415800-66432000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:66415800-66432200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr17:66415800-66432200	Strong transcription	Adipose Nuclei	Adipose
12	chr17:66415800-66432200	Strong transcription	Brain Hippocampus Middle	brain
13	chr17:66415800-66432200	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:66415800-66432200	Strong transcription	Placenta	Placenta
15	chr17:66415800-66432200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr17:66415800-66432400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr17:66415800-66433600	Weak transcription	Small Intestine	intestine
18	chr17:66416000-66432200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr17:66416000-66432200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr17:66416000-66432200	Strong transcription	Osteobl	bone
21	chr17:66416000-66432400	Strong transcription	Brain Substantia Nigra	brain
22	chr17:66416000-66432400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:66416200-66432400	Strong transcription	Rectal Smooth Muscle	rectum
24	chr17:66416200-66432600	Strong transcription	Brain Cingulate Gyrus	brain
25	chr17:66416400-66432200	Strong transcription	Colonic Mucosa	Colon
26	chr17:66416600-66432000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:66416600-66432200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:66416600-66432400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:66416800-66431600	Strong transcription	Lung	lung
30	chr17:66416800-66432000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr17:66416800-66432200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr17:66417000-66431400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:66417000-66432000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:66417000-66432000	Strong transcription	Fetal Muscle Leg	muscle
35	chr17:66417400-66432000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr17:66417600-66432000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:66417800-66432600	Strong transcription	Fetal Stomach	stomach
38	chr17:66418400-66432000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr17:66419000-66431200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr17:66419000-66432400	Strong transcription	Spleen	Spleen
41	chr17:66419200-66429800	Strong transcription	Brain Angular Gyrus	brain
42	chr17:66419200-66432000	Strong transcription	Brain Anterior Caudate	brain
43	chr17:66419200-66432200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:66419200-66432200	Strong transcription	Right Ventricle	heart
45	chr17:66419400-66432400	Strong transcription	Fetal Intestine Small	intestine
46	chr17:66419400-66432600	Strong transcription	Aorta	Aorta
47	chr17:66420800-66432200	Strong transcription	Ovary	ovary
48	chr17:66420800-66446400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr17:66420800-66451800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr17:66421200-66430800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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