Variant report

Variant	rs2525110
Chromosome Location	chr17:46042365-46042366
allele	A/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
ENSG00000167183	Chromatin interaction
ENSG00000108465	Chromatin interaction

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

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

rs_ID	r²[population]
rs11079802	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs11651753	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16949418	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs16949720	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2002136	0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2325748	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2428608	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2525095	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2525109	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];0.95[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs2875735	0.95[CHB][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	0.96[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];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2525110	SKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2525110	MRPL10	cis	Whole Blood	GTEx

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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