Variant report

Variant	rs2292699
Chromosome Location	chr17:45362295-45362296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45361920..45363647-chr17:45365032..45367345,2	MCF-7	breast:
2	chr17:45335188..45337634-chr17:45361564..45364329,3	K562	blood:
3	chr17:45329396..45331554-chr17:45361431..45363714,2	K562	blood:
4	chr17:45335188..45337634-chr17:45361564..45363925,2	K562	blood:
5	chr17:45360332..45367497-chr17:45367923..45374401,11	K562	blood:

Variant related genes	Relation type
ENSG00000259207	Chromatin interaction
ENSG00000259753	Chromatin interaction
ENSG00000238419	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1000232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs15908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16941801	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2015729	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851807	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4525555	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs4629024	0.80[GIH][hapmap];0.89[TSI][hapmap]
rs56327427	0.98[ASN][1000 genomes]
rs7209700	0.83[YRI][hapmap]
rs7212751	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214468	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7217710	0.82[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7218632	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073827	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs8074348	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs999323	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2292699	KRT32	cis	parietal	SCAN
rs2292699	C17orf57	cis	cerebellum	SCAN
rs2292699	SNX11	cis	parietal	SCAN
rs2292699	NPEPPS	cis	parietal	SCAN
rs2292699	C17orf57	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45354600-45372000	Weak transcription	Esophagus	oesophagus
2	chr17:45356800-45377200	Weak transcription	Fetal Intestine Large	intestine
3	chr17:45357200-45363800	Weak transcription	Fetal Heart	heart
4	chr17:45357200-45371600	Weak transcription	Right Ventricle	heart
5	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
6	chr17:45357800-45365800	Weak transcription	Ovary	ovary
7	chr17:45357800-45365800	Weak transcription	HSMMtube	muscle
8	chr17:45357800-45369400	Weak transcription	Fetal Intestine Small	intestine
9	chr17:45358200-45363600	Weak transcription	Spleen	Spleen
10	chr17:45358200-45363800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr17:45358200-45364000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:45358200-45365000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:45358200-45366000	Weak transcription	Right Atrium	heart
14	chr17:45358200-45367600	Weak transcription	Adipose Nuclei	Adipose
15	chr17:45358200-45371800	Weak transcription	Colonic Mucosa	Colon
16	chr17:45358200-45377200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr17:45358400-45362400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:45358400-45363600	Weak transcription	HSMM	muscle
19	chr17:45358400-45365800	Weak transcription	NH-A	brain
20	chr17:45358400-45366000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr17:45358600-45364000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr17:45358600-45371000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:45358800-45363600	Weak transcription	NHLF	lung
24	chr17:45358800-45364000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:45358800-45366000	Weak transcription	Lung	lung
26	chr17:45359000-45363000	Weak transcription	K562	blood
27	chr17:45359000-45363400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr17:45359000-45371600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr17:45359000-45372000	Weak transcription	Left Ventricle	heart
30	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:45359200-45363200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr17:45359400-45363600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr17:45359800-45362800	Strong transcription	HUVEC	blood vessel
34	chr17:45359800-45371200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr17:45360000-45364600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:45360000-45366000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:45360400-45371800	Strong transcription	Colon Smooth Muscle	Colon
38	chr17:45360600-45373800	Strong transcription	Fetal Stomach	stomach
39	chr17:45360800-45371800	Strong transcription	Fetal Muscle Leg	muscle
40	chr17:45361400-45370000	Strong transcription	Aorta	Aorta
41	chr17:45361400-45371400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr17:45361800-45362600	Strong transcription	NHDF-Ad	bronchial
43	chr17:45361800-45363200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:45361800-45367400	Strong transcription	Placenta	Placenta
45	chr17:45361800-45368200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:45362000-45362600	Strong transcription	Osteobl	bone
47	chr17:45362000-45363000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:45362000-45363200	Enhancers	Liver	Liver
49	chr17:45362000-45363800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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