Variant report

Variant	rs7249368
Chromosome Location	chr19:40200767-40200768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10407647	0.89[YRI][hapmap]
rs10410864	0.82[AFR][1000 genomes]
rs10755	0.85[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap]
rs1126158	0.83[ASW][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs2286759	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]
rs4132248	0.82[AFR][1000 genomes]
rs4803286	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4830	0.83[ASW][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs61213408	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6508903	0.89[YRI][hapmap]
rs6508904	0.82[AFR][1000 genomes]
rs7254368	0.89[YRI][hapmap]
rs7254761	0.93[YRI][hapmap]
rs7258833	0.83[ASW][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs8102588	0.82[AFR][1000 genomes]
rs8104035	0.83[ASW][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3332670	chr19:40181720-40297955	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7249368	CEACAM21	cis	parietal	SCAN
rs7249368	LGALS14	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40197200-40200800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:40198000-40200800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr19:40199400-40201200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:40200000-40201800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr19:40200200-40201800	Enhancers	GM12878-XiMat	blood
6	chr19:40200600-40201200	Genic enhancers	Placenta	Placenta
7	chr19:40200600-40201600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr19:40200600-40202400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:40200600-40202400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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