Variant report

Variant	rs10408199
Chromosome Location	chr19:37547659-37547660
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10401380	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10401525	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10401561	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10402050	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10404069	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404981	0.85[CEU][hapmap]
rs10405372	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10406612	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10407014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407224	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10407265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410594	0.89[CEU][hapmap];0.86[YRI][hapmap]
rs10410905	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10411037	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10411176	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs10412236	0.91[EUR][1000 genomes]
rs10413101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413304	0.82[EUR][1000 genomes]
rs10414107	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10414227	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416960	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs10417545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10418314	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419174	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419845	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10422428	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10424841	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10425441	0.82[EUR][1000 genomes]
rs10426093	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11084873	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12972146	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12975706	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12978093	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12983153	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13346284	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1617883	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1624293	1.00[CEU][hapmap]
rs1628959	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1644702	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1644704	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16971850	0.85[CEU][hapmap]
rs17707101	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs2385412	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28462002	0.91[EUR][1000 genomes]
rs28631881	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28660259	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34193103	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34915391	0.86[EUR][1000 genomes]
rs35080624	0.81[ASN][1000 genomes]
rs35522655	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35655645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816391	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs4473303	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4805198	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4805207	0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4805208	1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4806380	0.88[YRI][hapmap]
rs4806406	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806414	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62108899	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62109879	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6510583	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246473	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247758	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249696	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259878	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8101338	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8107654	0.81[ASN][1000 genomes]
rs9749562	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	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
14	nsv911653	chr19:37482151-37556673	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
15	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
16	nsv960832	chr19:37519841-37553181	ZNF genes & repeats Weak transcription Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases
17	nsv960888	chr19:37539063-37553181	ZNF genes & repeats Strong transcription Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10408199	ZNF420	cis	lymphoblastoid	seeQTL
rs10408199	AXL	cis	cerebellum	SCAN
rs10408199	XRCC1	cis	parietal	SCAN
rs10408199	SNRPD2	cis	parietal	SCAN
rs10408199	PAFAH1B3	cis	cerebellum	SCAN
rs10408199	CEACAM16	cis	cerebellum	SCAN
rs10408199	MEGF8	cis	cerebellum	SCAN
rs10408199	SERTAD3	cis	parietal	SCAN
rs10408199	VASP	cis	parietal	SCAN
rs10408199	ITPKC	cis	cerebellum	SCAN
rs10408199	EXOSC5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37545000-37550200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr19:37545800-37551600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:37546200-37548000	ZNF genes & repeats	Pancreas	Pancrea
4	chr19:37546200-37549600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr19:37546200-37550800	ZNF genes & repeats	Spleen	Spleen
6	chr19:37546200-37552400	ZNF genes & repeats	Liver	Liver
7	chr19:37546400-37551800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:37546400-37552400	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:37546600-37548200	ZNF genes & repeats	Gastric	stomach
10	chr19:37546800-37550000	ZNF genes & repeats	Fetal Lung	lung
11	chr19:37546800-37551400	ZNF genes & repeats	Fetal Stomach	stomach
12	chr19:37547000-37548400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:37547200-37547800	Weak transcription	Right Ventricle	heart
14	chr19:37547200-37551000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:37547400-37551200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:37547600-37548800	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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