Variant report

Variant	rs4880745
Chromosome Location	chr10:1018585-1018586
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1011250..1013274-chr10:1018564..1020381,2	K562	blood:
2	chr10:1016732..1019141-chr10:1025032..1027093,3	MCF-7	breast:
3	chr10:1016935..1018860-chr10:1032660..1034729,2	K562	blood:
4	chr10:976040..979233-chr10:1016379..1022615,6	MCF-7	breast:
5	chr10:1015043..1019353-chr10:1030351..1034278,6	MCF-7	breast:
6	chr10:986461..988686-chr10:1017171..1019953,2	MCF-7	breast:
7	chr10:949273..951052-chr10:1017196..1019797,2	K562	blood:
8	chr10:975132..982582-chr10:1010670..1022073,17	MCF-7	breast:
9	chr10:1015119..1019104-chr10:1032459..1035516,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000205740	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000229869	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10795305	0.84[JPT][hapmap]
rs10904593	0.84[JPT][hapmap]
rs11253542	0.83[JPT][hapmap]
rs11253543	0.84[JPT][hapmap]
rs11599792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12411376	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12415759	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12570412	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12570742	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871624	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2170142	0.84[JPT][hapmap]
rs2242271	0.89[CEU][hapmap];0.84[CHD][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs2306404	0.84[JPT][hapmap]
rs2306406	0.84[JPT][hapmap]
rs2306408	0.84[JPT][hapmap]
rs2306409	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35249079	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3750729	0.80[JPT][hapmap]
rs4880749	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4880752	0.88[EUR][1000 genomes]
rs4880757	0.80[JPT][hapmap]
rs4881543	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4881546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4881547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4881548	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4881553	0.87[EUR][1000 genomes]
rs61833304	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7069123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7071250	0.89[JPT][hapmap]
rs7075050	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7094916	0.89[JPT][hapmap]
rs7097976	0.84[JPT][hapmap]
rs7099607	0.89[CEU][hapmap];0.82[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7898019	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7900801	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7906595	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs947403	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
14	esv2753756	chr10:985264-1052950	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv5521	chr10:986842-1031352	Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv1037193	chr10:989533-1019630	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	nsv525014	chr10:1013535-1024214	Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4880745	WDR37	cis	parietal	SCAN
rs4880745	C10orf110	cis	cerebellum	SCAN
rs4880745	GTPBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4880745	WDR37	cis	cerebellum	SCAN
rs4880745	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:998800-1026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:1012400-1019000	Enhancers	Placenta	Placenta
3	chr10:1013600-1018800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:1014200-1020600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr10:1014600-1018600	Weak transcription	Brain Angular Gyrus	brain
6	chr10:1014800-1022400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:1015800-1019800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr10:1016000-1021600	Enhancers	Stomach Mucosa	stomach
9	chr10:1016200-1020800	Enhancers	Fetal Intestine Large	intestine
10	chr10:1017000-1018800	Weak transcription	Gastric	stomach
11	chr10:1017000-1019800	Weak transcription	Osteobl	bone
12	chr10:1017000-1020400	Enhancers	Fetal Lung	lung
13	chr10:1017000-1022400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:1017000-1022600	Weak transcription	Ovary	ovary
15	chr10:1017400-1018800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:1017600-1023800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:1017800-1021400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:1017800-1022600	Weak transcription	HSMM	muscle
19	chr10:1017800-1022600	Weak transcription	NHLF	lung
20	chr10:1017800-1023600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:1017800-1024600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr10:1017800-1024800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:1018000-1020000	Weak transcription	Pancreas	Pancrea
24	chr10:1018000-1021200	Enhancers	HepG2	liver
25	chr10:1018000-1022400	Weak transcription	Fetal Muscle Leg	muscle
26	chr10:1018000-1022400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:1018000-1023800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr10:1018000-1024400	Weak transcription	Adipose Nuclei	Adipose
29	chr10:1018200-1019000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:1018400-1025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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