Variant report

Variant	rs2525109
Chromosome Location	chr17:46042327-46042328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr17:46042264-46042520	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46041301..46044030-chr17:46048146..46051314,3	MCF-7	breast:
2	chr17:46042235..46044126-chr17:46090847..46093838,2	K562	blood:
3	chr17:46039634..46045111-chr17:46046533..46049867,10	K562	blood:
4	chr17:46040813..46045111-chr17:46046677..46049654,4	K562	blood:
5	chr17:46030056..46036320-chr17:46039939..46045055,5	K562	blood:

No data

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11079802	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs11651753	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16949418	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs16949720	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs2002136	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs2325748	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2428608	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2525095	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2525110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597169	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs2875735	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3764398	0.86[ASN][1000 genomes]
rs3826396	0.95[ASN][1000 genomes]
rs4793738	0.97[ASN][1000 genomes]
rs4794331	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs57768342	0.92[ASN][1000 genomes]
rs61665404	0.97[ASN][1000 genomes]
rs7207225	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7220104	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs72823505	0.93[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2525109	SKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2525109	CBX1	cis	cerebellum	SCAN
rs2525109	PNPO	cis	cerebellum	SCAN
rs2525109	PNPO	cis	parietal	SCAN
rs2525109	CDK5RAP3	cis	parietal	SCAN
rs2525109	COASY	cis	parietal	SCAN
rs2525109	MRPL10	cis	Whole Blood	GTEx
rs2525109	RPRML	cis	parietal	SCAN
rs2525109	CDK5RAP3	cis	cerebellum	SCAN
rs2525109	RAB5C	cis	parietal	SCAN
rs2525109	SP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr17:46036000-46047200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr17:46036200-46043400	Weak transcription	A549	lung
11	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
13	chr17:46037800-46042400	Weak transcription	Placenta	Placenta
14	chr17:46037800-46047400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:46037800-46047400	Enhancers	Fetal Intestine Small	intestine
16	chr17:46037800-46047800	Enhancers	Fetal Intestine Large	intestine
17	chr17:46038000-46043000	Weak transcription	Esophagus	oesophagus
18	chr17:46038000-46043800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr17:46038000-46046400	Weak transcription	K562	blood
20	chr17:46038400-46042400	Weak transcription	HepG2	liver
21	chr17:46038600-46043400	Enhancers	Colonic Mucosa	Colon
22	chr17:46039200-46042800	Weak transcription	Gastric	stomach
23	chr17:46039200-46043000	Weak transcription	Pancreas	Pancrea
24	chr17:46039400-46042400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:46039600-46042800	Weak transcription	Ovary	ovary
26	chr17:46039600-46047600	Weak transcription	Primary T cells from cord blood	blood
27	chr17:46040400-46042400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr17:46041200-46043200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr17:46041600-46042600	Enhancers	Stomach Mucosa	stomach
30	chr17:46042200-46042800	Enhancers	Small Intestine	intestine

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