Variant report

Variant	rs10517833
Chromosome Location	chr4:166170390-166170391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr4:166170007-166170642	MCF10A-Er-Src	breast:	n/a	chr4:166170254-166170263 chr4:166170253-166170262 chr4:166170252-166170263 chr4:166170138-166170145
2	FOS	chr4:166169993-166170640	MCF10A-Er-Src	breast:	n/a	chr4:166170312-166170321
3	FOS	chr4:166169987-166170558	MCF10A-Er-Src	breast:	n/a	chr4:166170312-166170321
4	STAT3	chr4:166170073-166170508	MCF10A-Er-Src	breast:	n/a	chr4:166170254-166170263 chr4:166170253-166170262 chr4:166170252-166170263 chr4:166170138-166170145
5	MYC	chr4:166170082-166170429	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr4:166170198-166170399	Hela-S3	cervix:	n/a	chr4:166170340-166170351 chr4:166170338-166170351
7	CEBPB	chr4:166170151-166170442	IMR90	lung:	n/a	chr4:166170340-166170351 chr4:166170338-166170351
8	E2F4	chr4:166170130-166170557	MCF10A-Er-Src	breast:	n/a	chr4:166170311-166170320
9	MYC	chr4:166170093-166170426	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr4:166170001-166170443	MCF10A-Er-Src	breast:	n/a	chr4:166170312-166170321
11	POLR2A	chr4:166170162-166170565	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr4:166170007-166170515	MCF10A-Er-Src	breast:	n/a	chr4:166170312-166170321
13	STAT3	chr4:166170069-166170625	MCF10A-Er-Src	breast:	n/a	chr4:166170254-166170263 chr4:166170253-166170262 chr4:166170252-166170263 chr4:166170138-166170145
14	STAT3	chr4:166169732-166170642	MCF10A-Er-Src	breast:	n/a	chr4:166170254-166170263 chr4:166170253-166170262 chr4:166170252-166170263 chr4:166170138-166170145

Variant related genes	Relation type
RNU4-87P	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10213277	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11725167	0.84[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11726415	1.00[CHB][hapmap]
rs12108446	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1530043	1.00[CHB][hapmap]
rs17046216	1.00[CHB][hapmap]
rs17488289	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17488436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17488534	1.00[CHB][hapmap]
rs17488569	1.00[CHB][hapmap]
rs17488814	0.89[ASN][1000 genomes]
rs17488835	0.89[ASN][1000 genomes]
rs17488877	0.89[ASN][1000 genomes]
rs17585396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17585515	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17585550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986031	1.00[ASN][1000 genomes]
rs28472332	0.87[EUR][1000 genomes]
rs28678592	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs36230153	0.89[ASN][1000 genomes]
rs3901486	1.00[ASN][1000 genomes]
rs4588420	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs55648903	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55650232	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55806488	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56022310	1.00[ASN][1000 genomes]
rs56058696	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104713	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144732	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56287687	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326646	1.00[ASN][1000 genomes]
rs56370618	1.00[ASN][1000 genomes]
rs56387271	0.89[ASN][1000 genomes]
rs56407727	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56410965	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57162477	1.00[ASN][1000 genomes]
rs58426709	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58781490	0.83[EUR][1000 genomes]
rs6831119	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853219	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72699595	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72699598	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72701606	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72701608	1.00[ASN][1000 genomes]
rs72701616	0.85[EUR][1000 genomes]
rs72701655	0.89[ASN][1000 genomes]
rs72701660	0.89[ASN][1000 genomes]
rs72701663	0.89[ASN][1000 genomes]
rs7676311	0.82[EUR][1000 genomes]
rs7680096	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv966337	chr4:166157947-166176361	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10517833	KLHL2	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
2	chr4:166130400-166176800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:166130600-166200800	Weak transcription	Lung	lung
4	chr4:166131600-166196800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:166132200-166193800	Weak transcription	Fetal Brain Female	brain
6	chr4:166136000-166176800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:166137800-166194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:166138400-166185600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:166142800-166176800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:166144000-166176000	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:166144600-166218800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:166144800-166176200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:166147000-166176400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:166151200-166176000	Weak transcription	Dnd41	blood
15	chr4:166152000-166176600	Weak transcription	Fetal Stomach	stomach
16	chr4:166156200-166199200	Weak transcription	Ovary	ovary
17	chr4:166159400-166173200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:166159400-166175800	Weak transcription	GM12878-XiMat	blood
19	chr4:166159800-166170400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:166159800-166176000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:166161200-166176800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:166161600-166176400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr4:166162200-166170400	Weak transcription	NHEK	skin
24	chr4:166167400-166177000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:166168400-166170400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr4:166168800-166170400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr4:166168800-166170600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr4:166168800-166170600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:166169200-166170600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr4:166169400-166170600	Enhancers	HMEC	breast
31	chr4:166169600-166170600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:166170000-166170400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:166170000-166170800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr4:166170000-166172200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr4:166170000-166175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:166170000-166175800	Weak transcription	HUVEC	blood vessel
37	chr4:166170000-166176200	Weak transcription	Primary B cells from cord blood	blood
38	chr4:166170000-166176400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:166170000-166210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:166170200-166176000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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