Variant report

Variant	rs1258168
Chromosome Location	chr10:50951259-50951260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11101218	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1125165	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1258169	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258176	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1258178	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1258179	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1258181	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1258182	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1258184	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1258201	0.89[JPT][hapmap];0.80[MEX][hapmap]
rs1258204	0.89[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap]
rs1258228	0.81[EUR][1000 genomes]
rs1258241	0.85[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs1258243	0.86[EUR][1000 genomes]
rs1258245	0.93[EUR][1000 genomes]
rs1258246	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258247	0.86[EUR][1000 genomes]
rs1258249	0.86[EUR][1000 genomes]
rs1258250	0.86[EUR][1000 genomes]
rs1258251	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1258252	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258255	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258256	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1258258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1258260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258323	0.85[CEU][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs1258326	0.85[CEU][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1258329	0.85[EUR][1000 genomes]
rs1258330	0.86[EUR][1000 genomes]
rs1268722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1268723	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1270562	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1271629	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13736	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1625258	0.86[EUR][1000 genomes]
rs1659305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889729	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4372365	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6537552	0.83[CHD][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6816	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv895378	chr10:50801342-50955649	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1048905	chr10:50928727-51019190	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3318018	chr10:50947746-50952444	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases
7	esv3318029	chr10:50947746-50952444	Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
8	esv3401087	chr10:50948446-50954144	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3346477	chr10:50949996-50952794	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1258168	TMPRSS3	trans	lymphoblastoid	seeQTL
rs1258168	DRGX	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50940400-50953400	Weak transcription	Brain Hippocampus Middle	brain
2	chr10:50940600-50966000	Strong transcription	Liver	Liver
3	chr10:50941000-50951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr10:50941200-50965400	Weak transcription	Brain Germinal Matrix	brain
5	chr10:50943000-50956400	Strong transcription	Brain Anterior Caudate	brain
6	chr10:50943200-50969400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr10:50943400-50956200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:50943800-50956000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:50944000-50969400	Weak transcription	Brain Substantia Nigra	brain
10	chr10:50944400-50952400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:50944800-50951600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:50945400-50953000	Weak transcription	Ovary	ovary
13	chr10:50946200-50951600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:50946200-50955200	Weak transcription	Fetal Brain Female	brain
15	chr10:50947200-50952400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr10:50947800-50960400	Strong transcription	Brain Angular Gyrus	brain
17	chr10:50948000-50956600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:50948600-50955600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:50948800-50956600	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr10:50949000-50953800	Weak transcription	Gastric	stomach
21	chr10:50949600-50956200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr10:50950000-50954800	Weak transcription	Spleen	Spleen
23	chr10:50950000-50955000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr10:50950200-50952600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr10:50950200-50954600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr10:50950400-50951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr10:50950400-50953400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr10:50950400-50955600	Strong transcription	Fetal Intestine Small	intestine
29	chr10:50950600-50952200	Weak transcription	Fetal Heart	heart
30	chr10:50950600-50953400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:50950600-50955600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr10:50950800-50952600	Strong transcription	Pancreas	Pancrea
33	chr10:50950800-50955200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr10:50951000-50955600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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