Variant report

Variant	rs2074301
Chromosome Location	chr19:19381715-19381716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19375808..19378765-chr19:19380089..19382167,3	K562	blood:
2	chr19:19378511..19382101-chr19:19389076..19392249,3	K562	blood:

Variant related genes	Relation type
ENSG00000213996	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1009136	0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1010207	0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs10401969	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs10402661	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10403731	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10407952	0.89[ASN][1000 genomes]
rs10409234	0.87[ASN][1000 genomes]
rs10418051	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419245	0.92[ASN][1000 genomes]
rs10419672	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10421505	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10426780	0.89[ASN][1000 genomes]
rs11085259	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11085261	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666553	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12459676	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460764	0.87[ASN][1000 genomes]
rs12972397	0.93[CEU][hapmap];0.80[JPT][hapmap]
rs12973258	0.82[CEU][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap]
rs12976025	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12977524	0.93[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs12977937	0.87[ASN][1000 genomes]
rs12979148	0.80[AFR][1000 genomes]
rs12981974	0.91[EUR][1000 genomes]
rs12982276	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12983137	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12985655	0.82[ASN][1000 genomes]
rs13964	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs15622	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1859287	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017964	0.92[ASN][1000 genomes]
rs2023882	0.89[ASN][1000 genomes]
rs2023883	0.90[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074089	0.89[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs2074090	0.89[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2074091	0.82[ASN][1000 genomes]
rs2074296	0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2074298	0.89[ASN][1000 genomes]
rs2074299	0.92[ASN][1000 genomes]
rs2074300	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074303	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2074550	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2074551	0.87[ASN][1000 genomes]
rs2163804	0.86[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2269873	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2285627	0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2285628	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285859	0.89[ASN][1000 genomes]
rs2301668	0.90[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2301669	0.82[ASN][1000 genomes]
rs2301671	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301784	0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2301786	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2315022	0.89[ASN][1000 genomes]
rs2315025	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2905423	0.81[ASN][1000 genomes]
rs2905424	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2905425	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2965191	0.82[ASN][1000 genomes]
rs2965193	0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965198	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3764567	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs4808193	0.83[ASN][1000 genomes]
rs4808194	0.93[CEU][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808196	0.80[AMR][1000 genomes]
rs4808199	0.93[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs4808937	0.89[ASN][1000 genomes]
rs4808938	0.89[ASN][1000 genomes]
rs4808939	0.94[ASN][1000 genomes]
rs4808940	0.85[ASN][1000 genomes]
rs4808941	0.85[ASN][1000 genomes]
rs4808942	0.90[ASN][1000 genomes]
rs4808960	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs62135552	0.86[ASN][1000 genomes]
rs6511026	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6511028	0.89[ASN][1000 genomes]
rs67720221	0.92[ASN][1000 genomes]
rs7246748	0.86[ASN][1000 genomes]
rs7247309	0.86[ASN][1000 genomes]
rs7250368	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7254230	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7254748	0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7254927	0.89[ASN][1000 genomes]
rs7258508	0.83[ASN][1000 genomes]
rs7259434	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs735273	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs757000	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757001	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs769267	0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs8101938	0.92[ASN][1000 genomes]
rs8103197	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs8103496	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8105094	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8105984	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8108647	0.83[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304960	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs968525	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911306	chr19:19366643-19391838	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2074301	KIAA0892	cis	multi-tissue	Pritchard
rs2074301	SLC25A42	cis	cerebellum	SCAN
rs2074301	ZNF826P	cis	cerebellum	SCAN
rs2074301	ZNF492	cis	cerebellum	SCAN
rs2074301	ZNF714	cis	parietal	SCAN
rs2074301	ZNF826P	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19373000-19384000	Weak transcription	Pancreas	Pancrea
2	chr19:19374000-19383400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:19374000-19383400	Weak transcription	Right Atrium	heart
4	chr19:19374200-19383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:19374400-19383200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:19374800-19381800	Strong transcription	Fetal Intestine Small	intestine
7	chr19:19374800-19383200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:19377800-19381800	Weak transcription	Fetal Intestine Large	intestine
9	chr19:19380200-19382600	Weak transcription	Liver	Liver
10	chr19:19380800-19381800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:19381200-19383400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:19381400-19381800	Genic enhancers	Duodenum Mucosa	Duodenum
13	chr19:19381400-19382000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:19381400-19382200	Enhancers	Small Intestine	intestine
15	chr19:19381600-19383000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:19381600-19383000	Enhancers	Stomach Mucosa	stomach
17	chr19:19381600-19383200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:19381600-19385600	Weak transcription	Brain Angular Gyrus	brain
19	chr19:19381600-19387600	Weak transcription	K562	blood

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