Variant report

Variant	rs912480
Chromosome Location	chr10:98378250-98378251
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98376151..98378929-chr10:98479647..98482597,2	K562	blood:
2	chr10:98376679..98380080-chr10:98381155..98385346,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227032	Chromatin interaction
ENSG00000155629	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1018604	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1018605	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1051450	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10736114	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882811	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10882813	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10882815	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10882826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882827	0.81[AFR][1000 genomes]
rs10882828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188815	0.83[JPT][hapmap]
rs11188817	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs11188822	0.84[JPT][hapmap]
rs11188825	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs11188831	0.83[JPT][hapmap]
rs11188833	0.83[JPT][hapmap]
rs11188844	0.83[JPT][hapmap]
rs11188847	0.82[CHD][hapmap]
rs11188853	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188854	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188857	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11188858	0.87[ASN][1000 genomes]
rs1132913	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1132914	0.83[JPT][hapmap]
rs12219275	0.83[JPT][hapmap]
rs12220047	0.81[JPT][hapmap]
rs12414612	0.83[JPT][hapmap]
rs12416646	0.83[JPT][hapmap]
rs12775533	0.83[JPT][hapmap]
rs12779720	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1324255	0.83[JPT][hapmap]
rs1324256	0.83[JPT][hapmap]
rs1324258	0.87[CEU][hapmap]
rs1324261	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1408367	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1983831	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031326	0.83[JPT][hapmap]
rs33964467	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs35779764	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs36098523	0.84[AFR][1000 genomes]
rs3689	0.83[JPT][hapmap]
rs3748234	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3748235	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789957	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs3818389	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4146727	0.82[CHD][hapmap]
rs4485036	0.83[JPT][hapmap]
rs4534508	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4917742	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]
rs4919029	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs4919032	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4919040	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7069429	0.83[JPT][hapmap]
rs7071044	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs7071224	0.83[JPT][hapmap]
rs7074516	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs7086213	0.83[JPT][hapmap]
rs7091606	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs7101320	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs713251	0.83[CHD][hapmap]
rs727329	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7448	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs7478356	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7914154	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7919739	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs8578	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs927639	0.87[CEU][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9633703	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs9664749	0.83[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3333231	chr10:98375362-98379560	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs912480	NPM1P26	cis	Esophagus Muscularis	GTEx
rs912480	NPM1P26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:67 , 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	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr10:98370800-98378600	Weak transcription	Brain Substantia Nigra	brain
16	chr10:98371000-98378800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:98371000-98382600	Strong transcription	Spleen	Spleen
18	chr10:98371000-98388600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr10:98371000-98389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:98371800-98378600	Weak transcription	Colonic Mucosa	Colon
21	chr10:98372200-98388600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr10:98374000-98378600	Weak transcription	Gastric	stomach
23	chr10:98374000-98378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:98374000-98379000	Weak transcription	Lung	lung
25	chr10:98374200-98378400	Weak transcription	Fetal Intestine Large	intestine
26	chr10:98374400-98378600	Weak transcription	HepG2	liver
27	chr10:98374400-98390200	Weak transcription	Small Intestine	intestine
28	chr10:98374800-98379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:98375000-98378400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr10:98375200-98378400	Weak transcription	HSMM	muscle
31	chr10:98375200-98379400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:98375600-98378400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:98375600-98380800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr10:98375800-98390200	Weak transcription	Adipose Nuclei	Adipose
35	chr10:98376000-98378400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr10:98376400-98380400	Enhancers	Fetal Heart	heart
37	chr10:98376400-98381200	Enhancers	Ovary	ovary
38	chr10:98376600-98378400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:98376600-98380400	Enhancers	Left Ventricle	heart
40	chr10:98376800-98381000	Enhancers	Right Atrium	heart
41	chr10:98377000-98379600	Enhancers	HSMMtube	muscle
42	chr10:98377000-98380800	Enhancers	Fetal Lung	lung
43	chr10:98377200-98379200	Enhancers	Psoas Muscle	Psoas
44	chr10:98377200-98379600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr10:98377200-98380000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:98377200-98380000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr10:98377200-98384400	Enhancers	Stomach Mucosa	stomach
48	chr10:98377400-98378400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr10:98377400-98378400	Enhancers	K562	blood
50	chr10:98377400-98379000	Enhancers	Brain Germinal Matrix	brain

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