Variant report

Variant	rs1324259
Chromosome Location	chr10:98347993-98347994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr10:98347853-98348079	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:98347973-98348041	K562	blood:	n/a	n/a
3	POLR2A	chr10:98347783-98348099	HepG2	liver:	n/a	n/a
4	FOXA1	chr10:98347623-98348108	HepG2	liver:	n/a	n/a
5	HEY1	chr10:98347743-98348185	HepG2	liver:	n/a	n/a
6	WRNIP1	chr10:98347833-98348012	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:98345375-98348129	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:98344907-98348506	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr10:98345903-98348124	GM19099	blood:	n/a	n/a
10	GATA3	chr10:98347523-98348017	T-47D	breast:	n/a	n/a
11	POLR2A	chr10:98345206-98348070	MCF10A-Er-Src	breast:	n/a	n/a
12	TBP	chr10:98347269-98348081	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:98347496-98348152	HepG2	liver:	n/a	n/a
14	POLR2A	chr10:98347844-98348041	HepG2	liver:	n/a	n/a
15	POLR2A	chr10:98345380-98348086	Raji	blood:	n/a	n/a
16	RFX5	chr10:98347963-98348019	K562	blood:	n/a	n/a
17	HCFC1	chr10:98345973-98348623	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr10:98345566-98348126	GM12878	blood:	n/a	n/a
19	TBP	chr10:98346989-98348169	Hela-S3	cervix:	n/a	n/a
20	TBP	chr10:98347850-98348179	HepG2	liver:	n/a	n/a
21	MTA3	chr10:98346777-98348058	GM12878	blood:	n/a	n/a
22	CHD1	chr10:98344949-98348090	IMR90	lung:	n/a	chr10:98346594-98346604
23	POLR2A	chr10:98344788-98348079	HepG2	liver:	n/a	n/a
24	RCOR1	chr10:98346714-98348125	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:98346136-98347996	GM12878	blood:	n/a	n/a
26	FOXA2	chr10:98347830-98348083	HepG2	liver:	n/a	n/a
27	FOS	chr10:98347789-98347997	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr10:98347594-98348144	HepG2	liver:	n/a	n/a
29	POLR2A	chr10:98347853-98348104	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr10:98345216-98348146	HepG2	liver:	n/a	n/a
31	ZNF384	chr10:98347905-98348012	GM12878	blood:	n/a	n/a
32	EP300	chr10:98347872-98348029	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:98347948-98348000	MCF-7	breast:	n/a	n/a
34	POLR2A	chr10:98345061-98348128	PBDE	blood:	n/a	n/a
35	CEBPB	chr10:98346644-98348129	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr10:98345560-98348114	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:98336275..98339517-chr10:98344498..98348223,6	MCF-7	breast:
2	chr10:98347309..98348851-chr10:98354166..98356679,2	K562	blood:
3	chr10:98344586..98349024-chr10:98390080..98394763,4	MCF-7	breast:

No data

Variant related genes	Relation type
TM9SF3	TF binding region
ENSG00000155629	Chromatin interaction
ENSG00000077147	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10128106	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1018604	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1018605	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051450	0.94[ASN][1000 genomes]
rs1063605	0.94[ASN][1000 genomes]
rs10736114	0.81[ASN][1000 genomes]
rs10882809	0.82[ASN][1000 genomes]
rs10882811	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882813	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882815	0.82[ASN][1000 genomes]
rs10882817	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882821	0.88[ASN][1000 genomes]
rs10882822	0.85[AMR][1000 genomes]
rs10882827	0.81[ASN][1000 genomes]
rs10882828	0.81[ASN][1000 genomes]
rs11188809	0.82[ASN][1000 genomes]
rs11188810	0.82[ASN][1000 genomes]
rs11188811	0.82[ASN][1000 genomes]
rs11188813	0.82[ASN][1000 genomes]
rs11188814	0.82[ASN][1000 genomes]
rs11188815	0.82[ASN][1000 genomes]
rs11188817	0.82[ASN][1000 genomes]
rs11188821	0.82[ASN][1000 genomes]
rs11188822	0.82[ASN][1000 genomes]
rs11188825	0.82[ASN][1000 genomes]
rs11188827	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188831	0.91[ASN][1000 genomes]
rs11188832	0.91[ASN][1000 genomes]
rs11188833	0.91[ASN][1000 genomes]
rs11188840	0.91[ASN][1000 genomes]
rs11188842	0.94[ASN][1000 genomes]
rs11188844	0.94[ASN][1000 genomes]
rs11188847	0.84[ASN][1000 genomes]
rs11188848	0.87[ASN][1000 genomes]
rs11188853	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188854	0.82[EUR][1000 genomes]
rs1132913	0.82[ASN][1000 genomes]
rs1132914	0.82[ASN][1000 genomes]
rs1156035	0.82[ASN][1000 genomes]
rs1156036	0.82[ASN][1000 genomes]
rs11814010	0.82[ASN][1000 genomes]
rs12218847	0.82[ASN][1000 genomes]
rs12219275	0.91[ASN][1000 genomes]
rs12220047	0.91[ASN][1000 genomes]
rs12221143	0.82[ASN][1000 genomes]
rs12221262	0.82[ASN][1000 genomes]
rs12414612	0.82[ASN][1000 genomes]
rs12415048	0.82[ASN][1000 genomes]
rs12416646	0.82[ASN][1000 genomes]
rs12761817	0.82[ASN][1000 genomes]
rs12766248	0.82[ASN][1000 genomes]
rs12775533	0.88[ASN][1000 genomes]
rs12776810	0.94[ASN][1000 genomes]
rs12779720	0.82[ASN][1000 genomes]
rs1324255	0.82[ASN][1000 genomes]
rs1324256	0.91[ASN][1000 genomes]
rs1324261	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408367	0.91[ASN][1000 genomes]
rs17391547	0.82[ASN][1000 genomes]
rs17482382	0.82[ASN][1000 genomes]
rs2011190	0.82[ASN][1000 genomes]
rs2025451	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031326	0.91[ASN][1000 genomes]
rs2031329	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861555	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33964467	0.88[ASN][1000 genomes]
rs35779764	0.88[ASN][1000 genomes]
rs36098523	0.87[ASN][1000 genomes]
rs3689	0.82[ASN][1000 genomes]
rs3748234	0.81[ASN][1000 genomes]
rs3748236	0.85[ASN][1000 genomes]
rs3748237	0.94[ASN][1000 genomes]
rs3789957	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789958	0.82[ASN][1000 genomes]
rs3818389	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4146727	0.81[ASN][1000 genomes]
rs4485036	0.82[ASN][1000 genomes]
rs4534508	0.82[ASN][1000 genomes]
rs4917742	0.81[ASN][1000 genomes]
rs4919029	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4919032	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919037	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919040	0.80[EUR][1000 genomes]
rs58305369	0.87[ASN][1000 genomes]
rs61858194	0.88[ASN][1000 genomes]
rs61858494	0.82[ASN][1000 genomes]
rs61859300	0.94[ASN][1000 genomes]
rs7069429	0.82[ASN][1000 genomes]
rs7070686	0.94[ASN][1000 genomes]
rs7071044	0.94[ASN][1000 genomes]
rs7071224	0.82[ASN][1000 genomes]
rs7071881	0.94[ASN][1000 genomes]
rs7073017	0.87[ASN][1000 genomes]
rs7073682	0.87[ASN][1000 genomes]
rs7074516	0.94[ASN][1000 genomes]
rs7082873	0.91[ASN][1000 genomes]
rs7085389	0.94[ASN][1000 genomes]
rs7086213	0.94[ASN][1000 genomes]
rs7086240	0.82[ASN][1000 genomes]
rs7087478	0.82[ASN][1000 genomes]
rs7091606	0.87[ASN][1000 genomes]
rs7097291	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101320	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs713251	0.82[ASN][1000 genomes]
rs727329	0.82[ASN][1000 genomes]
rs7448	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7478356	0.80[EUR][1000 genomes]
rs7919739	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8578	0.94[ASN][1000 genomes]
rs927639	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9633703	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9664749	0.82[ASN][1000 genomes]
rs9664955	0.82[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	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	esv3358283	chr10:98345587-98348135	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1324259	NPM1P26	cis	Esophagus Muscularis	GTEx
rs1324259	NPM1P26	cis	Adipose Subcutaneous	GTEx
rs1324259	NPM1P26	cis	Stomach	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98344800-98348000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:98345200-98348000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:98345200-98348000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr10:98345400-98348000	Active TSS	Aorta	Aorta
5	chr10:98345600-98348000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr10:98345600-98348000	Active TSS	Fetal Muscle Trunk	muscle
7	chr10:98345800-98348000	Active TSS	Colonic Mucosa	Colon
8	chr10:98345800-98348600	Active TSS	Psoas Muscle	Psoas
9	chr10:98347000-98348000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr10:98347000-98348000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:98347000-98348000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr10:98347000-98348000	Flanking Active TSS	Dnd41	blood
13	chr10:98347000-98348000	Flanking Active TSS	NH-A	brain
14	chr10:98347000-98348200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:98347000-98348200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:98347000-98354600	Weak transcription	Spleen	Spleen
17	chr10:98347200-98348000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr10:98347200-98348000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr10:98347200-98348000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr10:98347200-98348000	Flanking Active TSS	Fetal Thymus	thymus
21	chr10:98347200-98348000	Flanking Active TSS	HMEC	breast
22	chr10:98347200-98348200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:98347200-98348200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr10:98347200-98348200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr10:98347200-98348200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:98347200-98348200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:98347200-98348200	Flanking Active TSS	Fetal Kidney	kidney
28	chr10:98347200-98348200	Flanking Active TSS	HUVEC	blood vessel
29	chr10:98347200-98348200	Flanking Active TSS	NHLF	lung
30	chr10:98347200-98349000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr10:98347400-98348000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr10:98347400-98348000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr10:98347400-98348000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:98347400-98348000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr10:98347400-98348000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr10:98347400-98348000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr10:98347400-98348000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:98347400-98348000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr10:98347400-98348000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr10:98347400-98348000	Flanking Active TSS	Fetal Intestine Large	intestine
41	chr10:98347400-98348000	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr10:98347400-98348000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr10:98347400-98348200	Flanking Active TSS	Liver	Liver
44	chr10:98347400-98348200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr10:98347400-98348200	Flanking Active TSS	NHEK	skin
46	chr10:98347400-98348600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr10:98347400-98348600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr10:98347400-98348800	Flanking Active TSS	GM12878-XiMat	blood
49	chr10:98347400-98358800	Weak transcription	Pancreas	Pancrea
50	chr10:98347600-98348000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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