Variant report

Variant	rs4802583
Chromosome Location	chr19:39025341-39025342
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39022005..39025490-chr19:39026869..39030422,4	K562	blood:
2	chr19:39024830..39027065-chr19:39108421..39111246,2	MCF-7	breast:
3	chr19:39018304..39021212-chr19:39024595..39027619,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104814	Chromatin interaction
ENSG00000268055	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000269445	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004795	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]
rs1004796	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]
rs10404936	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10408694	1.00[CEU][hapmap]
rs10413936	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10415792	0.88[EUR][1000 genomes]
rs12459024	1.00[ASN][1000 genomes]
rs12459749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459780	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]
rs12459845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461789	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984412	1.00[ASN][1000 genomes]
rs13345914	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2287731	1.00[TSI][hapmap]
rs2287734	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2292797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292800	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]
rs2292801	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[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];1.00[ASN][1000 genomes]
rs2303041	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2368477	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2960350	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34754809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[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];0.97[ASN][1000 genomes]
rs3786844	1.00[TSI][hapmap]
rs3829976	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs45613041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802582	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]
rs4802584	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]
rs4802587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802589	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802608	1.00[AFR][1000 genomes]
rs4802618	1.00[CEU][hapmap]
rs6508809	1.00[CEU][hapmap]
rs750437	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs8107386	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription 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	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	22 gene(s)	inside rSNPs	diseases
9	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4802583	CXCL9	trans	brain	seeQTL
rs4802583	DPF1	cis	brain	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr19:38963000-39033000	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
4	chr19:38997600-39025400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:39001000-39025600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:39006200-39025400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:39006800-39025600	Weak transcription	Brain Substantia Nigra	brain
8	chr19:39007000-39025600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:39007800-39025400	Weak transcription	Brain Anterior Caudate	brain
10	chr19:39019400-39025600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:39019800-39025400	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:39019800-39029000	Weak transcription	Fetal Brain Male	brain
13	chr19:39020600-39027800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:39021000-39029200	Strong transcription	HSMMtube	muscle
15	chr19:39025000-39026200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:39025000-39026400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr19:39025000-39026400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr19:39025000-39026600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
19	chr19:39025000-39026600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
20	chr19:39025000-39026600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
21	chr19:39025000-39027600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
22	chr19:39025200-39025400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:39025200-39025600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:39025200-39025800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:39025200-39026000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:39025200-39026000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:39025200-39026000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:39025200-39026400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr19:39025200-39026400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
30	chr19:39025200-39026600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
31	chr19:39025200-39026600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
32	chr19:39025200-39026600	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr19:39025200-39026600	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr19:39025200-39026600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
35	chr19:39025200-39027200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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