Variant report

Variant	rs1324258
Chromosome Location	chr10:98347504-98347505
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10128106	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1018604	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1018605	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1051450	0.90[ASN][1000 genomes]
rs1063605	0.90[ASN][1000 genomes]
rs10736114	0.88[CEU][hapmap]
rs10882811	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882813	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882817	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882821	0.84[ASN][1000 genomes]
rs10882826	0.87[CEU][hapmap]
rs10882828	0.90[CEU][hapmap]
rs11188827	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11188831	0.87[ASN][1000 genomes]
rs11188832	0.87[ASN][1000 genomes]
rs11188833	0.87[ASN][1000 genomes]
rs11188840	0.87[ASN][1000 genomes]
rs11188842	0.90[ASN][1000 genomes]
rs11188844	0.90[ASN][1000 genomes]
rs11188848	0.83[ASN][1000 genomes]
rs11188853	0.87[ASN][1000 genomes]
rs11188856	0.91[CEU][hapmap]
rs12219275	0.87[ASN][1000 genomes]
rs12220047	0.87[ASN][1000 genomes]
rs12775533	0.84[ASN][1000 genomes]
rs12776810	0.90[ASN][1000 genomes]
rs1324256	0.87[ASN][1000 genomes]
rs1324259	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1324261	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1408367	0.87[ASN][1000 genomes]
rs2025451	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2031326	0.87[ASN][1000 genomes]
rs2031329	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2861555	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33964467	0.84[ASN][1000 genomes]
rs35779764	0.84[ASN][1000 genomes]
rs36098523	0.83[ASN][1000 genomes]
rs3748236	0.81[ASN][1000 genomes]
rs3748237	0.90[ASN][1000 genomes]
rs3789957	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818389	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917742	0.88[CEU][hapmap]
rs4919029	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4919032	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4919037	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4919040	0.80[CEU][hapmap]
rs58305369	0.83[ASN][1000 genomes]
rs61858194	0.84[ASN][1000 genomes]
rs61859300	0.90[ASN][1000 genomes]
rs7070686	0.90[ASN][1000 genomes]
rs7071044	0.90[ASN][1000 genomes]
rs7071881	0.90[ASN][1000 genomes]
rs7073017	0.83[ASN][1000 genomes]
rs7073682	0.83[ASN][1000 genomes]
rs7074516	0.90[ASN][1000 genomes]
rs7082873	0.87[ASN][1000 genomes]
rs7085389	0.90[ASN][1000 genomes]
rs7086213	0.90[ASN][1000 genomes]
rs7091606	0.83[ASN][1000 genomes]
rs7097291	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7101320	0.86[ASN][1000 genomes]
rs7448	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7919739	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8578	0.90[ASN][1000 genomes]
rs912480	0.87[CEU][hapmap]
rs927639	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9633703	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	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
3	esv3446584	chr10:98345712-98347935	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1324258	NPM1P26	cis	Esophagus Muscularis	GTEx
rs1324258	NPM1P26	cis	Adipose Subcutaneous	GTEx
rs1324258	NPM1P26	cis	Stomach	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98344400-98347600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr10:98344400-98347600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr10:98344600-98347600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:98344600-98347600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:98344600-98347800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr10:98344600-98347800	Active TSS	Right Ventricle	heart
7	chr10:98344800-98347600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:98344800-98347600	Active TSS	NHDF-Ad	bronchial
9	chr10:98344800-98348000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:98345000-98347600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr10:98345000-98347600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:98345000-98347600	Active TSS	A549	lung
13	chr10:98345000-98347800	Active TSS	Right Atrium	heart
14	chr10:98345000-98347800	Active TSS	Thymus	Thymus
15	chr10:98345200-98347600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr10:98345200-98347600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:98345200-98347800	Active TSS	Ovary	ovary
18	chr10:98345200-98348000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr10:98345200-98348000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr10:98345400-98347600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:98345400-98347600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:98345400-98347600	Active TSS	Left Ventricle	heart
23	chr10:98345400-98347600	Active TSS	Small Intestine	intestine
24	chr10:98345400-98347600	Active TSS	Stomach Mucosa	stomach
25	chr10:98345400-98347800	Active TSS	Placenta Amnion	Placenta Amnion
26	chr10:98345400-98347800	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr10:98345400-98348000	Active TSS	Aorta	Aorta
28	chr10:98345600-98347600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr10:98345600-98347600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:98345600-98347600	Active TSS	Hela-S3	cervix
31	chr10:98345600-98348000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr10:98345600-98348000	Active TSS	Fetal Muscle Trunk	muscle
33	chr10:98345800-98347600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr10:98345800-98347600	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr10:98345800-98347600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:98345800-98347600	Active TSS	Brain Substantia Nigra	brain
37	chr10:98345800-98347600	Active TSS	Colon Smooth Muscle	Colon
38	chr10:98345800-98347600	Active TSS	Fetal Lung	lung
39	chr10:98345800-98347800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr10:98345800-98348000	Active TSS	Colonic Mucosa	Colon
41	chr10:98345800-98348600	Active TSS	Psoas Muscle	Psoas
42	chr10:98346000-98347600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:98346000-98347600	Active TSS	Brain Angular Gyrus	brain
44	chr10:98346000-98347600	Active TSS	Brain Anterior Caudate	brain
45	chr10:98346000-98347600	Active TSS	Brain Cingulate Gyrus	brain
46	chr10:98346000-98347600	Active TSS	Brain Hippocampus Middle	brain
47	chr10:98346000-98347600	Active TSS	Fetal Stomach	stomach
48	chr10:98346000-98347600	Active TSS	Rectal Smooth Muscle	rectum
49	chr10:98346000-98347600	Active TSS	Stomach Smooth Muscle	stomach
50	chr10:98346000-98347600	Active TSS	K562	blood

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