Variant report

Variant	rs10425441
Chromosome Location	chr19:37670648-37670649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10401380	0.82[EUR][1000 genomes]
rs10401525	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10401561	0.82[EUR][1000 genomes]
rs10402050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10404069	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10404973	0.82[EUR][1000 genomes]
rs10405372	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10406612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes]
rs10407014	0.82[EUR][1000 genomes]
rs10407224	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10407265	0.82[EUR][1000 genomes]
rs10408199	0.82[EUR][1000 genomes]
rs10410905	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10411037	0.83[EUR][1000 genomes]
rs10411176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10412236	0.81[EUR][1000 genomes]
rs10413101	0.82[EUR][1000 genomes]
rs10413304	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414107	0.82[EUR][1000 genomes]
rs10414983	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10417545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10418314	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419174	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10422428	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10424841	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10426093	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11084873	0.83[CEU][hapmap];0.88[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972146	0.84[CEU][hapmap];0.88[CHB][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12975869	0.81[EUR][1000 genomes]
rs12978093	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12983153	0.88[CHB][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13346284	0.82[EUR][1000 genomes]
rs1617883	0.83[EUR][1000 genomes]
rs2385412	0.82[EUR][1000 genomes]
rs28462002	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28631881	0.80[EUR][1000 genomes]
rs28660259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28701616	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34193103	0.82[EUR][1000 genomes]
rs34915391	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35522655	0.82[EUR][1000 genomes]
rs35655645	0.82[EUR][1000 genomes]
rs4473303	0.86[ASN][1000 genomes]
rs4805198	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4805207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4805208	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806406	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4806414	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62108899	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62109879	0.83[EUR][1000 genomes]
rs7246473	0.82[EUR][1000 genomes]
rs7247758	0.82[EUR][1000 genomes]
rs7259878	0.82[EUR][1000 genomes]
rs8101338	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8111936	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8112011	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	esv3433517	chr19:37643755-37675928	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10425441	DMPK	cis	parietal	SCAN
rs10425441	CBLC	cis	parietal	SCAN
rs10425441	MEGF8	cis	cerebellum	SCAN
rs10425441	AXL	cis	cerebellum	SCAN
rs10425441	SNRPD2	cis	parietal	SCAN
rs10425441	PAFAH1B3	cis	cerebellum	SCAN
rs10425441	VASP	cis	parietal	SCAN
rs10425441	CEACAM16	cis	cerebellum	SCAN
rs10425441	ZNF420	cis	lymphoblastoid	seeQTL
rs10425441	EXOSC5	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37663600-37673200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:37664000-37673000	Weak transcription	Fetal Brain Female	brain
3	chr19:37664000-37673400	Weak transcription	Fetal Brain Male	brain
4	chr19:37664200-37673200	Weak transcription	Fetal Heart	heart
5	chr19:37664200-37675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:37668000-37686000	ZNF genes & repeats	Liver	Liver
7	chr19:37670000-37681200	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:37670400-37672800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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