Variant report

Variant	rs4917742
Chromosome Location	chr10:98374426-98374427
allele	C/G
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	chr10:98374366-98374701	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr10:98374331-98374654	MCF10A-Er-Src	breast:	n/a	chr10:98374426-98374435
3	GATA2	chr10:98374275-98374601	K562	blood:	n/a	n/a
4	GATA1	chr10:98373904-98374813	PBDE	blood:	n/a	chr10:98374091-98374102
5	EP300	chr10:98374280-98374682	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr10:98374256-98374589	K562	blood:	n/a	n/a
7	FOS	chr10:98374243-98374670	MCF10A-Er-Src	breast:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
8	FOSL2	chr10:98374165-98374770	SK-N-SH	brain:	n/a	chr10:98374426-98374434 chr10:98374425-98374435 chr10:98374425-98374435
9	POLR2A	chr10:98374272-98374433	MCF10A-Er-Src	breast:	n/a	n/a
10	GABPA	chr10:98374248-98374446	K562	blood:	n/a	n/a
11	RCOR1	chr10:98374035-98374613	K562	blood:	n/a	n/a
12	FOSL1	chr10:98374170-98374571	K562	blood:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
13	EP300	chr10:98374316-98374645	SK-N-SH_RA	brain:	n/a	n/a
14	NR2F2	chr10:98374175-98374570	K562	blood:	n/a	n/a
15	PBX3	chr10:98374233-98374675	SK-N-SH	brain:	n/a	n/a
16	STAT3	chr10:98374367-98374650	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr10:98374357-98374671	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:98374241-98374603	K562	blood:	n/a	n/a
19	TEAD4	chr10:98374184-98374651	K562	blood:	n/a	n/a
20	FOS	chr10:98374255-98374721	MCF10A-Er-Src	breast:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
21	NR2F2	chr10:98374106-98374647	K562	blood:	n/a	n/a
22	TAL1	chr10:98373912-98374662	K562	blood:	n/a	chr10:98374437-98374452 chr10:98374437-98374452 chr10:98374440-98374451 chr10:98374437-98374452
23	POLR2A	chr10:98373556-98374859	GM12878	blood:	n/a	n/a
24	FOS	chr10:98374257-98374723	HUVEC	blood vessel:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
25	PBX3	chr10:98374180-98374749	SK-N-SH	brain:	n/a	n/a
26	FOS	chr10:98374252-98374623	MCF10A-Er-Src	breast:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
27	POLR2A	chr10:98374268-98374677	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr10:98374102-98374879	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr10:98374086-98376151	GM12878	blood:	n/a	n/a
30	TEAD4	chr10:98374162-98374604	K562	blood:	n/a	n/a
31	STAT3	chr10:98374332-98374664	MCF10A-Er-Src	breast:	n/a	n/a
32	NFIC	chr10:98374133-98374799	ECC-1	luminal epithelium:	n/a	chr10:98374476-98374493 chr10:98374466-98374494
33	MYC	chr10:98374331-98374619	MCF10A-Er-Src	breast:	n/a	chr10:98374426-98374435
34	FOSL1	chr10:98374290-98374503	K562	blood:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
35	FOS	chr10:98374181-98374810	MCF10A-Er-Src	breast:	n/a	chr10:98374426-98374434 chr10:98374424-98374435 chr10:98374425-98374435 chr10:98374425-98374435
36	NFIC	chr10:98374152-98374848	SK-N-SH	brain:	n/a	chr10:98374476-98374493 chr10:98374466-98374494
37	FOSL2	chr10:98374209-98374723	A549	lung:	n/a	chr10:98374426-98374434 chr10:98374425-98374435 chr10:98374425-98374435
38	NFIC	chr10:98374162-98374825	ECC-1	luminal epithelium:	n/a	chr10:98374476-98374493 chr10:98374466-98374494
39	TCF12	chr10:98374090-98374841	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:98341817..98344367-chr10:98373392..98375014,2	K562	blood:
2	chr10:98360613..98362809-chr10:98373002..98374950,2	K562	blood:
3	chr10:98345726..98350448-chr10:98373759..98376409,5	MCF-7	breast:
4	chr10:98373312..98375091-chr10:98382282..98385347,3	K562	blood:
5	chr10:98372394..98374938-chr10:98530168..98532928,2	MCF-7	breast:
6	chr10:98345541..98351057-chr10:98372487..98376675,6	K562	blood:
7	chr10:98367008..98370019-chr10:98371148..98375452,4	K562	blood:
8	chr10:98346216..98350490-chr10:98369688..98376085,7	K562	blood:
9	chr10:98346219..98349334-chr10:98373001..98374910,3	MCF-7	breast:

Variant related genes	Relation type
RNA5SP324	TF binding region
ENSG00000077147	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1018604	0.88[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1018605	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1051450	0.83[JPT][hapmap]
rs10736114	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882811	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10882813	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10882815	0.83[JPT][hapmap]
rs10882826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882827	0.82[ASN][1000 genomes]
rs10882828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188815	0.84[JPT][hapmap]
rs11188817	0.83[JPT][hapmap]
rs11188822	0.86[JPT][hapmap]
rs11188825	0.83[JPT][hapmap]
rs11188831	0.84[JPT][hapmap]
rs11188833	0.84[JPT][hapmap]
rs11188844	0.84[JPT][hapmap]
rs11188848	0.82[ASN][1000 genomes]
rs11188853	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188854	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188857	0.93[ASN][1000 genomes]
rs11188858	0.81[ASN][1000 genomes]
rs1132913	0.83[JPT][hapmap]
rs1132914	0.83[JPT][hapmap]
rs12219275	0.83[JPT][hapmap]
rs12220047	0.82[JPT][hapmap]
rs12414612	0.84[JPT][hapmap]
rs12416646	0.83[JPT][hapmap]
rs12775533	0.84[JPT][hapmap]
rs12779720	0.82[JPT][hapmap]
rs1324255	0.84[JPT][hapmap]
rs1324256	0.84[JPT][hapmap]
rs1324258	0.88[CEU][hapmap]
rs1324259	0.81[ASN][1000 genomes]
rs1324261	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1408367	0.83[JPT][hapmap]
rs1983831	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2025451	0.81[ASN][1000 genomes]
rs2031326	0.83[JPT][hapmap]
rs33964467	0.83[JPT][hapmap]
rs35779764	0.83[JPT][hapmap]
rs36098523	0.82[ASN][1000 genomes]
rs3689	0.84[JPT][hapmap]
rs3748234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3748235	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748236	0.83[ASN][1000 genomes]
rs3789957	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs3818389	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4146727	0.82[ASN][1000 genomes]
rs4485036	0.83[JPT][hapmap]
rs4534508	0.83[JPT][hapmap]
rs4919029	1.00[JPT][hapmap]
rs4919032	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4919037	0.81[ASN][1000 genomes]
rs4919040	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58305369	0.82[ASN][1000 genomes]
rs61858194	0.81[ASN][1000 genomes]
rs7069429	0.83[JPT][hapmap]
rs7071044	0.83[JPT][hapmap]
rs7071224	0.84[JPT][hapmap]
rs7073017	0.82[ASN][1000 genomes]
rs7073682	0.82[ASN][1000 genomes]
rs7074516	0.83[JPT][hapmap]
rs7082873	0.81[JPT][hapmap]
rs7086213	0.84[JPT][hapmap]
rs7091606	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7097291	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7101320	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs727329	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7448	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7478356	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7914154	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7919739	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs8578	0.83[JPT][hapmap]
rs912480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs927639	0.87[CEU][hapmap];0.92[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9633703	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs9664749	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv895909	chr10:98354924-98382165	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4917742	NPM1P26	cis	Stomach	GTEx
rs4917742	NPM1P26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr10:98352400-98378600	Strong transcription	Liver	Liver
3	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
9	chr10:98360400-98392800	Weak transcription	Thymus	Thymus
10	chr10:98362200-98389200	Strong transcription	Primary B cells from cord blood	blood
11	chr10:98363800-98392600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:98366000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:98366600-98392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:98367200-98375000	Enhancers	Stomach Mucosa	stomach
15	chr10:98367200-98376200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:98367400-98375000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr10:98367400-98376200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:98368800-98377800	Weak transcription	Brain Anterior Caudate	brain
20	chr10:98370600-98375800	Weak transcription	Ovary	ovary
21	chr10:98370800-98378600	Weak transcription	Brain Substantia Nigra	brain
22	chr10:98371000-98378800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr10:98371000-98382600	Strong transcription	Spleen	Spleen
24	chr10:98371000-98388600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:98371000-98389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:98371200-98375000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr10:98371800-98378600	Weak transcription	Colonic Mucosa	Colon
28	chr10:98372200-98377400	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:98372200-98388600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr10:98372400-98375400	Weak transcription	Adipose Nuclei	Adipose
31	chr10:98372600-98376000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:98373200-98375000	Enhancers	K562	blood
33	chr10:98373200-98375600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:98373400-98374600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:98373400-98374600	Enhancers	A549	lung
36	chr10:98373400-98374800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr10:98373400-98375000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:98373400-98375000	Enhancers	NH-A	brain
39	chr10:98373400-98375200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:98373400-98375200	Enhancers	HSMMtube	muscle
41	chr10:98373400-98375200	Enhancers	NHDF-Ad	bronchial
42	chr10:98373400-98375400	Strong transcription	Pancreas	Pancrea
43	chr10:98373400-98378000	Enhancers	Right Ventricle	heart
44	chr10:98373600-98374800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:98373600-98375000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:98373600-98375200	Enhancers	HSMM	muscle
47	chr10:98373800-98374800	Enhancers	Duodenum Mucosa	Duodenum
48	chr10:98373800-98375000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr10:98374000-98374800	Weak transcription	Left Ventricle	heart
50	chr10:98374000-98375000	Enhancers	Fetal Heart	heart

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