Variant report

Variant	rs998732
Chromosome Location	chr19:19378671-19378672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19378396-19379639	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19336338..19339154-chr19:19378323..19380714,2	K562	blood:
2	chr19:19371179..19375166-chr19:19377084..19380673,3	K562	blood:
3	chr19:19374128..19376226-chr19:19377973..19380781,2	MCF-7	breast:
4	chr19:19378511..19382101-chr19:19389076..19392249,3	K562	blood:

Variant related genes	Relation type
TM6SF2	TF binding region
ENSG00000130287	Chromatin interaction
ENSG00000187664	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10401714	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10403273	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10407933	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10422893	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10423874	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1064395	1.00[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11555053	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1557723	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1560687	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs17216041	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17751061	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1989867	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2010506	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011503	0.81[ASW][hapmap];0.81[CEU][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060274	0.81[CEU][hapmap]
rs2060275	0.81[CEU][hapmap]
rs2074302	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2315023	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2860494	0.81[AMR][1000 genomes]
rs2916070	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2965184	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2965186	0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2965190	0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2965195	0.81[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2965201	0.81[CEU][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs35854118	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4239639	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808932	0.94[EUR][1000 genomes]
rs4808933	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808934	1.00[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808944	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808951	0.81[CEU][hapmap]
rs55762233	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55765017	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55822665	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56044734	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56135441	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56144632	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56212061	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56278919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57436187	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511027	1.00[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7257875	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72999030	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72999059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72999063	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72999068	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs754256	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs756997	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs756999	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8100097	0.86[EUR][1000 genomes]
rs8105642	0.81[CEU][hapmap]
rs8108777	0.94[EUR][1000 genomes]
rs8110171	0.81[CEU][hapmap]
rs8110250	0.81[CEU][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs998732	GATAD2A	cis	parietal	SCAN
rs998732	YJEFN3	cis	cerebellum	SCAN
rs998732	LOC440518	cis	parietal	SCAN
rs998732	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs998732	LSM4	cis	cerebellum	SCAN
rs998732	DDX49	cis	cerebellum	SCAN
rs998732	OCEL1	cis	parietal	SCAN
rs998732	IL12RB1	cis	parietal	SCAN

Chromatin state (count:12 , 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	chr19:19374400-19381400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr19:19374400-19383200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:19374800-19381800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:19374800-19383200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:19375000-19378800	Strong transcription	Liver	Liver
10	chr19:19377400-19380400	Weak transcription	Fetal Stomach	stomach
11	chr19:19377600-19380800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:19377800-19381800	Weak transcription	Fetal Intestine Large	intestine

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