Variant report

Variant	rs1018604
Chromosome Location	chr10:98341583-98341584
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	POLR2A	chr10:98341556-98342066	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:98341324-98342561	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98326952..98329299-chr10:98339860..98342406,2	K562	blood:
2	chr10:98340228..98344806-chr10:98344870..98348374,6	MCF-7	breast:

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

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10128106	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1018605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051450	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs1063605	0.94[ASN][1000 genomes]
rs10736114	0.88[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10882809	0.82[ASN][1000 genomes]
rs10882811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882815	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10882817	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882821	0.88[ASN][1000 genomes]
rs10882822	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10882826	0.87[CEU][hapmap];0.92[JPT][hapmap]
rs10882827	0.81[ASN][1000 genomes]
rs10882828	0.90[CEU][hapmap];1.00[JPT][hapmap];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	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188817	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188821	0.82[ASN][1000 genomes]
rs11188822	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188825	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188827	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188831	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs11188832	0.91[ASN][1000 genomes]
rs11188833	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs11188840	0.91[ASN][1000 genomes]
rs11188842	0.94[ASN][1000 genomes]
rs11188844	0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs11188847	0.84[ASN][1000 genomes]
rs11188848	0.87[ASN][1000 genomes]
rs11188853	0.91[ASN][1000 genomes]
rs11188856	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1132913	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1132914	0.83[JPT][hapmap];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	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs12220047	0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12221143	0.82[ASN][1000 genomes]
rs12221262	0.82[ASN][1000 genomes]
rs12414612	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12415048	0.82[ASN][1000 genomes]
rs12416646	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12761817	0.82[ASN][1000 genomes]
rs12766248	0.82[ASN][1000 genomes]
rs12775533	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12776810	0.94[ASN][1000 genomes]
rs12779720	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1324255	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1324256	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs1324258	1.00[CEU][hapmap]
rs1324259	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324261	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408367	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs17391547	0.82[ASN][1000 genomes]
rs17482382	0.82[ASN][1000 genomes]
rs1983831	0.92[JPT][hapmap]
rs2011190	0.82[ASN][1000 genomes]
rs2025451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031326	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs2031329	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861555	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33964467	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs35779764	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs36098523	0.87[ASN][1000 genomes]
rs3689	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3748234	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3748235	0.92[JPT][hapmap]
rs3748236	0.85[ASN][1000 genomes]
rs3748237	0.94[ASN][1000 genomes]
rs3789957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789958	0.82[ASN][1000 genomes]
rs3818389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4146727	0.81[ASN][1000 genomes]
rs4485036	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4534508	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4917742	0.88[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4919029	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4919032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919037	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919040	0.81[CEU][hapmap];0.85[CHB][hapmap]
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	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7070686	0.94[ASN][1000 genomes]
rs7071044	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7071224	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7071881	0.94[ASN][1000 genomes]
rs7073017	0.87[ASN][1000 genomes]
rs7073682	0.87[ASN][1000 genomes]
rs7074516	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7082873	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs7085389	0.94[ASN][1000 genomes]
rs7086213	0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs7086240	0.82[ASN][1000 genomes]
rs7087478	0.82[ASN][1000 genomes]
rs7091606	0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7097291	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101320	0.90[ASN][1000 genomes]
rs713251	0.82[ASN][1000 genomes]
rs727329	0.82[ASN][1000 genomes]
rs7448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914154	1.00[JPT][hapmap]
rs7919739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8578	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs912480	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs927639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9633703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9664749	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9664955	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1018604	NPM1P26	cis	Adipose Subcutaneous	GTEx
rs1018604	NPM1P26	cis	Stomach	GTEx
rs1018604	NPM1P26	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98276400-98343200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:98286600-98345600	Weak transcription	Esophagus	oesophagus
3	chr10:98290000-98344200	Weak transcription	Spleen	Spleen
4	chr10:98292600-98344800	Weak transcription	Brain Germinal Matrix	brain
5	chr10:98307800-98341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:98314400-98345600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:98320200-98344800	Weak transcription	HSMMtube	muscle
8	chr10:98320400-98341600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:98322200-98343400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr10:98324600-98345000	Weak transcription	Fetal Kidney	kidney
11	chr10:98326600-98341600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:98328000-98343200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:98329200-98345000	Weak transcription	Fetal Stomach	stomach
14	chr10:98329200-98345600	Weak transcription	Gastric	stomach
15	chr10:98329800-98344400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:98329800-98345200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:98331400-98344200	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:98331400-98344800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:98331600-98341600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:98331800-98345200	Weak transcription	Fetal Brain Male	brain
21	chr10:98332200-98341600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr10:98332200-98341600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr10:98332200-98341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr10:98332200-98345400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:98333400-98344000	Weak transcription	Primary B cells from cord blood	blood
26	chr10:98334800-98345600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:98335000-98341600	Weak transcription	Fetal Thymus	thymus
28	chr10:98335800-98344400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr10:98336000-98343600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:98336200-98342600	Enhancers	Fetal Intestine Large	intestine
31	chr10:98336200-98345200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr10:98336400-98341600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr10:98336400-98342600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr10:98336400-98343800	Weak transcription	NHEK	skin
35	chr10:98336400-98345200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr10:98336400-98345600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr10:98336600-98341600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr10:98336600-98341600	Weak transcription	Hela-S3	cervix
39	chr10:98336600-98343800	Enhancers	Primary T cells from cord blood	blood
40	chr10:98336600-98344800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:98336600-98345000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:98336800-98345000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:98336800-98345200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr10:98337000-98341600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:98337000-98343000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:98337000-98343800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr10:98337000-98344600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr10:98337200-98341600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:98337200-98341600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr10:98337200-98343000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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