Variant report

Variant	rs2288529
Chromosome Location	chr19:55665689-55665690
allele	C/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	chr19:55665658-55666039	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:55658330..55661734-chr19:55662329..55665982,4	MCF-7	breast:
2	chr19:55590321..55593325-chr19:55662374..55666146,3	K562	blood:

Variant related genes	Relation type
TNNT1	TF binding region
ENSG00000267577	TF binding region
ENSG00000105048	Chromatin interaction
ENSG00000131037	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10421953	0.82[ASN][1000 genomes]
rs10423713	0.83[ASN][1000 genomes]
rs1128712	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12459688	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459887	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459917	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459921	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459930	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12460445	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461148	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461170	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461195	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461202	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12462211	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17458	0.82[AMR][1000 genomes]
rs2071572	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071574	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278281	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288420	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs2288528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301278	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs3745922	0.82[AMR][1000 genomes]
rs3786867	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs3826887	0.84[AMR][1000 genomes]
rs3848618	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3859544	0.89[ASN][1000 genomes]
rs56666700	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56726774	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58017412	0.82[AMR][1000 genomes]
rs58218194	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58824375	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59663064	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60176657	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60799292	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61570139	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7248997	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7255625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs890871	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9710458	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2288529	SH2D2A	trans	brain	seeQTL
rs2288529	SLC5A7	trans	brain	seeQTL
rs2288529	GUCA1C	trans	brain	seeQTL
rs2288529	CRX	trans	brain	seeQTL
rs2288529	LRTM1	trans	brain	seeQTL
rs2288529	TTR	trans	brain	seeQTL
rs2288529	MATN2	trans	brain	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55661800-55667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr19:55662000-55667200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr19:55662000-55667400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr19:55662000-55667400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:55662000-55667400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:55663400-55667400	Weak transcription	A549	lung
7	chr19:55663600-55667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:55663600-55667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:55663600-55667400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:55663600-55667400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:55663800-55667200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:55664200-55666000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr19:55664400-55666400	Transcr. at gene 5' and 3'	Left Ventricle	heart
14	chr19:55664400-55667400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:55664800-55665800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:55664800-55666400	Active TSS	Right Atrium	heart
17	chr19:55665000-55666200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:55665200-55665800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:55665200-55666000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr19:55665200-55666000	Transcr. at gene 5' and 3'	Fetal Heart	heart
21	chr19:55665200-55666200	Genic enhancers	K562	blood
22	chr19:55665400-55666400	Transcr. at gene 5' and 3'	Right Ventricle	heart
23	chr19:55665400-55667200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:55665400-55667400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:55665400-55667400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:55665600-55665800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
27	chr19:55665600-55665800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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