Variant report

Variant	rs750438
Chromosome Location	chr19:39104375-39104376
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39102966..39104689-chr19:39107783..39109776,2	MCF-7	breast:
2	chr19:39098771..39100599-chr19:39103260..39105890,2	MCF-7	breast:
3	chr19:39103433..39106687-chr19:39106977..39109796,8	K562	blood:
4	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
5	chr19:39101758..39105983-chr19:39106668..39109959,5	K562	blood:

Variant related genes	Relation type
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10445564	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12977469	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13345885	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862371	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1978443	0.82[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2232992	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2287732	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287733	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786834	0.94[CEU][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4592774	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802618	0.81[LWK][hapmap]
rs60803495	0.98[ASN][1000 genomes]
rs62120354	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62120358	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251456	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs888994	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs750438	LYPD4	cis	parietal	SCAN
rs750438	AP2S1	cis	cerebellum	SCAN
rs750438	ZFP36	cis	parietal	SCAN
rs750438	SAE1	cis	parietal	SCAN
rs750438	SELV	cis	parietal	SCAN
rs750438	CYP2F1	cis	cerebellum	SCAN
rs750438	TMEM145	cis	parietal	SCAN
rs750438	PLAUR	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39087200-39107800	Weak transcription	Colonic Mucosa	Colon
2	chr19:39087400-39107400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr19:39087400-39108200	Weak transcription	Gastric	stomach
4	chr19:39087400-39108800	Weak transcription	Right Atrium	heart
5	chr19:39092600-39109000	Weak transcription	Small Intestine	intestine
6	chr19:39094000-39104600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:39094400-39105000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr19:39094600-39104400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:39094600-39106200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:39094800-39106400	Strong transcription	Primary T cells from cord blood	blood
11	chr19:39095400-39104400	Strong transcription	Thymus	Thymus
12	chr19:39095600-39104800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:39095600-39106000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:39095800-39106000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:39096200-39105200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:39096800-39108000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:39097800-39108200	Weak transcription	Fetal Intestine Small	intestine
18	chr19:39098600-39108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:39101600-39104400	Strong transcription	Primary B cells from cord blood	blood
20	chr19:39102000-39104400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:39102000-39108600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:39102200-39107200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:39102200-39107400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:39103000-39105200	Strong transcription	Dnd41	blood
25	chr19:39103200-39106600	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr19:39103200-39107000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:39103400-39106200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:39103600-39105000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:39103600-39107400	Weak transcription	Fetal Thymus	thymus
30	chr19:39103600-39108000	Weak transcription	Lung	lung
31	chr19:39103600-39108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:39104000-39106200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:39104000-39106400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr19:39104000-39106800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr19:39104000-39107000	Weak transcription	Spleen	Spleen
36	chr19:39104200-39104400	Enhancers	GM12878-XiMat	blood
37	chr19:39104200-39104600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr19:39104200-39106000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:39104200-39106200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr19:39104200-39106200	Enhancers	HepG2	liver
41	chr19:39104200-39106800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr19:39104200-39107200	Genic enhancers	Primary B cells from peripheral blood	blood

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