Variant report

Variant	rs4802122
Chromosome Location	chr19:42047924-42047925
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10406221	0.81[JPT][hapmap]
rs10406371	0.80[ASN][1000 genomes]
rs10406545	0.81[ASN][1000 genomes]
rs10406988	0.84[EUR][1000 genomes]
rs10410081	0.84[EUR][1000 genomes]
rs10420992	0.83[ASN][1000 genomes]
rs10423808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083627	0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11668699	0.84[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11669873	0.84[EUR][1000 genomes]
rs12150975	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12462897	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12609438	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12973063	0.89[GIH][hapmap]
rs12983999	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1860255	0.85[JPT][hapmap]
rs2191019	0.81[JPT][hapmap]
rs2286754	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302188	0.81[JPT][hapmap]
rs2317312	0.82[ASN][1000 genomes]
rs2317314	0.85[CHD][hapmap]
rs3826716	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802119	0.81[JPT][hapmap]
rs4802120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803475	0.83[EUR][1000 genomes]
rs4803476	0.83[EUR][1000 genomes]
rs4803479	0.82[ASN][1000 genomes]
rs4803481	0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs714106	0.81[JPT][hapmap]
rs7249258	0.87[GIH][hapmap]
rs7252454	0.93[ASN][1000 genomes]
rs7252624	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7255742	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7257282	0.99[ASN][1000 genomes]
rs7257565	0.83[ASN][1000 genomes]
rs8113621	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510767	chr19:41962486-42049165	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1055515	chr19:41968797-42057334	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv579602	chr19:42015468-42047924	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4802122	TMEM143	cis	parietal	SCAN
rs4802122	CEACAM21	cis	lymphoblastoid	seeQTL
rs4802122	R29124_1	cis	multi-tissue	Pritchard
rs4802122	CEACAM21	cis	multi-tissue	Pritchard
rs4802122	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs4802122	SYMPK	cis	cerebellum	SCAN
rs4802122	FLT3LG	cis	cerebellum	SCAN
rs4802122	CEACAM21	cis	Whole Blood	GTEx
rs4802122	CEACAM21	cis	Lymphoblastoid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42038600-42050800	Weak transcription	Spleen	Spleen
2	chr19:42042200-42048400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr19:42042200-42048600	Weak transcription	Primary T cells from cord blood	blood
4	chr19:42042200-42048600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:42042200-42048600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr19:42042800-42048600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr19:42043400-42052000	Weak transcription	Right Atrium	heart
8	chr19:42045000-42048400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:42046600-42048000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:42047000-42048600	Weak transcription	Primary B cells from cord blood	blood
11	chr19:42047000-42048600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:42047000-42048600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:42047000-42050600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:42047400-42050200	Weak transcription	GM12878-XiMat	blood

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