Variant report

Variant	rs17392013
Chromosome Location	chr10:98319815-98319816
allele	C/T
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	chr10:98319729-98320455	GM12892	blood:	n/a	n/a
2	POLR2A	chr10:98319772-98320085	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr10:98319793-98320173	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr10:98319656-98320475	GM12892	blood:	n/a	n/a
5	POLR2A	chr10:98318539-98320031	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:98319675-98320151	GM12891	blood:	n/a	n/a
7	POLR2A	chr10:98319701-98320329	GM12891	blood:	n/a	n/a
8	POLR2A	chr10:98319682-98319983	K562	blood:	n/a	n/a
9	POLR2A	chr10:98319769-98320274	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:98319653-98320443	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:98319761-98320086	GM12891	blood:	n/a	n/a
12	POLR2A	chr10:98319700-98320078	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
NPM1P26	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10736113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748682	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748683	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748684	1.00[ASN][1000 genomes]
rs10748685	1.00[ASN][1000 genomes]
rs10786302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786303	1.00[ASN][1000 genomes]
rs10786304	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11188835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11188849	1.00[ASN][1000 genomes]
rs11188850	1.00[ASN][1000 genomes]
rs11591933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592108	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592156	1.00[ASN][1000 genomes]
rs11592969	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11594403	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs11596148	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11598142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599054	1.00[ASN][1000 genomes]
rs12247652	1.00[ASN][1000 genomes]
rs17391197	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861626	1.00[ASN][1000 genomes]
rs3789955	1.00[ASW][hapmap]
rs4919030	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919039	1.00[ASN][1000 genomes]
rs55822182	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60471672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858218	1.00[ASN][1000 genomes]
rs61858493	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61858555	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858556	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584088	0.84[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7072865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7073125	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7073735	1.00[ASN][1000 genomes]
rs7093849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744363	1.00[ASN][1000 genomes]
rs7893530	0.84[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7897721	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923910	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912485	1.00[ASN][1000 genomes]
rs912486	1.00[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	nsv948151	chr10:98318755-98321287	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17392013	NDUFB8	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98274200-98328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:98274200-98328600	Weak transcription	Pancreas	Pancrea
3	chr10:98274200-98331200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:98276400-98343200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:98277800-98330400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr10:98286200-98323000	Weak transcription	Lung	lung
7	chr10:98286600-98338400	Weak transcription	Aorta	Aorta
8	chr10:98286600-98339400	Weak transcription	Brain Angular Gyrus	brain
9	chr10:98286600-98345600	Weak transcription	Esophagus	oesophagus
10	chr10:98290000-98344200	Weak transcription	Spleen	Spleen
11	chr10:98292600-98344800	Weak transcription	Brain Germinal Matrix	brain
12	chr10:98293600-98326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr10:98295400-98320800	Weak transcription	Fetal Heart	heart
14	chr10:98296200-98320600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr10:98297000-98329200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr10:98297200-98325000	Strong transcription	Placenta	Placenta
17	chr10:98297800-98324800	Strong transcription	Dnd41	blood
18	chr10:98298200-98322400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:98298400-98324600	Strong transcription	Primary B cells from cord blood	blood
20	chr10:98298600-98324600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr10:98298600-98325000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:98298600-98325200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr10:98298800-98320000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr10:98298800-98324200	Strong transcription	Fetal Thymus	thymus
25	chr10:98298800-98325600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:98299000-98325200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:98299400-98324200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr10:98300800-98322400	Strong transcription	HepG2	liver
29	chr10:98301200-98322600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr10:98304400-98325600	Weak transcription	NHLF	lung
31	chr10:98305400-98320400	Strong transcription	Fetal Intestine Large	intestine
32	chr10:98305400-98321600	Strong transcription	GM12878-XiMat	blood
33	chr10:98305400-98325000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr10:98305800-98325000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:98307400-98331200	Weak transcription	Fetal Brain Male	brain
36	chr10:98307600-98328200	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:98307600-98328600	Weak transcription	Right Ventricle	heart
38	chr10:98307800-98328600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr10:98307800-98331000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr10:98307800-98341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr10:98308000-98325600	Weak transcription	Brain Anterior Caudate	brain
42	chr10:98308000-98330800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr10:98308600-98320600	Weak transcription	Fetal Intestine Small	intestine
44	chr10:98308600-98320600	Strong transcription	HUVEC	blood vessel
45	chr10:98310000-98323400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:98310200-98320600	Strong transcription	A549	lung
47	chr10:98310400-98328400	Weak transcription	Fetal Brain Female	brain
48	chr10:98312800-98324600	Strong transcription	Primary T cells from cord blood	blood
49	chr10:98313000-98321200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:98313800-98328800	Weak transcription	Gastric	stomach

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