Variant report

Variant	rs1382125
Chromosome Location	chr8:54501069-54501070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:54500891..54501616-chr8:54619259..54619767,2	MCF-7	breast:
2	chr8:54500348..54501242-chr8:54721022..54722166,3	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10112441	0.86[ASN][1000 genomes]
rs10808882	1.00[ASN][1000 genomes]
rs10958375	1.00[ASN][1000 genomes]
rs10958376	1.00[ASN][1000 genomes]
rs10958377	0.92[ASN][1000 genomes]
rs10958378	0.92[ASN][1000 genomes]
rs10958379	0.86[ASN][1000 genomes]
rs10958380	0.86[ASN][1000 genomes]
rs10958386	0.86[ASN][1000 genomes]
rs11778297	0.81[ASN][1000 genomes]
rs11779176	0.86[ASN][1000 genomes]
rs11779309	0.94[ASN][1000 genomes]
rs11779641	1.00[ASN][1000 genomes]
rs11785377	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11785465	0.86[ASN][1000 genomes]
rs11785489	0.86[ASN][1000 genomes]
rs11987300	0.86[ASN][1000 genomes]
rs11995715	0.86[ASN][1000 genomes]
rs12547226	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549885	0.86[ASN][1000 genomes]
rs12549903	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];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12550388	0.86[ASN][1000 genomes]
rs13249182	0.86[ASN][1000 genomes]
rs13249232	0.86[ASN][1000 genomes]
rs13251373	0.86[ASN][1000 genomes]
rs13253006	0.86[ASN][1000 genomes]
rs13259310	1.00[ASN][1000 genomes]
rs13260243	0.86[ASN][1000 genomes]
rs13266723	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13268670	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13274248	0.86[ASN][1000 genomes]
rs13275215	0.86[ASN][1000 genomes]
rs1382123	1.00[ASN][1000 genomes]
rs1477960	1.00[ASN][1000 genomes]
rs1477964	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1477965	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1477966	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551910	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1551911	1.00[ASN][1000 genomes]
rs1551913	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2035197	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2086071	1.00[ASN][1000 genomes]
rs2086072	0.81[ASN][1000 genomes]
rs2086073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2086074	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs2086075	1.00[ASN][1000 genomes]
rs2169693	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2199590	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2199591	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521998	1.00[ASN][1000 genomes]
rs3919868	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3940882	1.00[ASN][1000 genomes]
rs4258030	1.00[ASN][1000 genomes]
rs4531078	1.00[ASN][1000 genomes]
rs4873261	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4873759	1.00[ASN][1000 genomes]
rs6415668	1.00[ASN][1000 genomes]
rs6415669	0.86[ASN][1000 genomes]
rs6415672	0.86[ASN][1000 genomes]
rs6415673	0.86[ASN][1000 genomes]
rs6415675	0.86[ASN][1000 genomes]
rs6473856	0.92[ASN][1000 genomes]
rs6473860	0.86[ASN][1000 genomes]
rs6473861	0.86[ASN][1000 genomes]
rs6473862	0.86[ASN][1000 genomes]
rs6473863	0.86[ASN][1000 genomes]
rs6473864	0.86[ASN][1000 genomes]
rs6473865	0.86[ASN][1000 genomes]
rs6473866	0.86[ASN][1000 genomes]
rs6473867	0.86[ASN][1000 genomes]
rs6473868	0.86[ASN][1000 genomes]
rs6473869	0.86[ASN][1000 genomes]
rs6473871	0.86[ASN][1000 genomes]
rs6473872	0.86[ASN][1000 genomes]
rs6473875	0.82[ASN][1000 genomes]
rs6473876	0.86[ASN][1000 genomes]
rs66931312	0.82[ASN][1000 genomes]
rs6983383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6989219	0.86[ASN][1000 genomes]
rs6989676	0.86[ASN][1000 genomes]
rs6990694	0.86[ASN][1000 genomes]
rs6991676	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991825	1.00[ASN][1000 genomes]
rs6996204	1.00[ASN][1000 genomes]
rs7008144	0.86[ASN][1000 genomes]
rs7009049	0.86[ASN][1000 genomes]
rs7010314	0.86[ASN][1000 genomes]
rs7386224	0.86[ASN][1000 genomes]
rs7387992	0.86[ASN][1000 genomes]
rs7388189	0.86[ASN][1000 genomes]
rs7388300	0.86[ASN][1000 genomes]
rs7388337	0.86[ASN][1000 genomes]
rs7459503	0.86[ASN][1000 genomes]
rs7459559	0.86[ASN][1000 genomes]
rs7459598	0.86[ASN][1000 genomes]
rs7460037	0.86[ASN][1000 genomes]
rs7460923	0.86[ASN][1000 genomes]
rs7460945	0.86[ASN][1000 genomes]
rs7461003	0.82[ASN][1000 genomes]
rs7461174	0.86[ASN][1000 genomes]
rs7461405	0.92[ASN][1000 genomes]
rs7461954	1.00[ASN][1000 genomes]
rs7462195	0.86[ASN][1000 genomes]
rs7462220	0.82[ASN][1000 genomes]
rs7462612	0.86[ASN][1000 genomes]
rs7462827	0.86[ASN][1000 genomes]
rs7462881	0.86[ASN][1000 genomes]
rs7462940	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463378	0.86[ASN][1000 genomes]
rs7463478	0.86[ASN][1000 genomes]
rs7463519	0.86[ASN][1000 genomes]
rs7464824	0.86[ASN][1000 genomes]
rs7465481	0.86[ASN][1000 genomes]
rs7465505	0.86[ASN][1000 genomes]
rs7465593	0.86[ASN][1000 genomes]
rs7465617	0.86[ASN][1000 genomes]
rs7465670	0.86[ASN][1000 genomes]
rs7820396	0.86[ASN][1000 genomes]
rs7825736	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7842388	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643813	0.86[ASN][1000 genomes]
rs9643814	0.86[ASN][1000 genomes]
rs978137	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs978139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs978140	1.00[ASN][1000 genomes]
rs979361	0.97[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	esv1813750	chr8:54471135-54528984	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2758159	chr8:54474589-54737473	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2759616	chr8:54474589-54737473	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1382125	SCN10A	trans	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54500000-54501400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr8:54500200-54501200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:54500200-54501200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr8:54500200-54501200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr8:54500200-54501200	Enhancers	HSMMtube	muscle
6	chr8:54500200-54501400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr8:54500400-54501200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr8:54500400-54501200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr8:54500400-54501200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr8:54500600-54501200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr8:54500600-54501200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr8:54500600-54501200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:54500600-54501200	Enhancers	Fetal Lung	lung
14	chr8:54500800-54501200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr8:54500800-54501200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr8:54500800-54501200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:54500800-54501200	Enhancers	Aorta	Aorta
18	chr8:54500800-54501200	Enhancers	Ovary	ovary
19	chr8:54500800-54501200	Enhancers	GM12878-XiMat	blood
20	chr8:54501000-54501200	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr8:54501000-54501400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:54501000-54502000	Weak transcription	Adipose Nuclei	Adipose
23	chr8:54501000-54502000	Weak transcription	Fetal Muscle Leg	muscle
24	chr8:54501000-54502000	Weak transcription	Pancreas	Pancrea
25	chr8:54501000-54504400	Weak transcription	Fetal Heart	heart

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