Variant report

Variant	rs17469719
Chromosome Location	chr3:43098330-43098331
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43092511..43095463-chr3:43096998..43098764,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10212191	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs10510736	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs1075408	1.00[AFR][1000 genomes]
rs13080201	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17390473	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17455509	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap]
rs17455760	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2001682	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2062517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2948619	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs35946401	1.00[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3953390	0.86[ASN][1000 genomes]
rs531888	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs532792	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs55701670	0.82[ASN][1000 genomes]
rs644534	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs66603383	0.82[ASN][1000 genomes]
rs67186096	0.88[ASN][1000 genomes]
rs6764648	0.83[CHB][hapmap]
rs6783218	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6793871	1.00[JPT][hapmap]
rs6794402	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs6806427	0.87[CHB][hapmap]
rs704903	0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs73074962	0.85[AFR][1000 genomes]
rs7616750	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7619227	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7624799	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs7633590	0.87[CHB][hapmap]
rs7634125	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7637698	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7643433	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs834177	0.87[CHB][hapmap]
rs872126	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9311332	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs9812262	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9821320	0.87[CHB][hapmap]
rs9848904	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs9863179	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17469719	CCDC13	cis	parietal	SCAN
rs17469719	ZDHHC3	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092200-43101000	Weak transcription	Pancreas	Pancrea
2	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:43094200-43099800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:43094200-43104200	Weak transcription	Gastric	stomach
6	chr3:43094400-43101400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:43094400-43101800	Weak transcription	Placenta	Placenta
8	chr3:43094400-43114800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:43095000-43101000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:43095000-43114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:43095600-43098400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:43095600-43100000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:43095800-43101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:43095800-43104400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:43096800-43100200	Strong transcription	Liver	Liver
17	chr3:43096800-43102600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:43097200-43099600	Weak transcription	Lung	lung
19	chr3:43097200-43104600	Weak transcription	Brain Substantia Nigra	brain
20	chr3:43097600-43098800	Strong transcription	Ovary	ovary
21	chr3:43097600-43101000	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:43098000-43099600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:43098000-43101200	Weak transcription	Fetal Stomach	stomach
24	chr3:43098200-43101000	Weak transcription	Stomach Smooth Muscle	stomach

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