Variant report

Variant	rs7249258
Chromosome Location	chr19:42007875-42007876
allele	A/T
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	REST	chr19:42006767-42007956	A549	lung:	n/a	n/a
2	FOXA2	chr19:42007320-42008140	A549	lung:	n/a	n/a
3	FOSL1	chr19:42007174-42007932	HCT-116	colon:	n/a	n/a
4	POLR2A	chr19:42006250-42007898	HUVEC	blood vessel:	n/a	n/a
5	TCF12	chr19:42006678-42008112	A549	lung:	n/a	n/a
6	FOS	chr19:42007874-42008336	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F6	chr19:42006624-42008253	A549	lung:	n/a	n/a
8	E2F6	chr19:42006864-42008112	A549	lung:	n/a	n/a
9	SP1	chr19:42006607-42007906	A549	lung:	n/a	n/a
10	POLR2A	chr19:42007375-42007925	HUVEC	blood vessel:	n/a	n/a
11	FOSL2	chr19:42006817-42008108	A549	lung:	n/a	n/a
12	HA-E2F1	chr19:42006937-42007975	MCF-7	breast:	n/a	n/a
13	MAX	chr19:42006587-42008026	A549	lung:	n/a	chr19:42007171-42007180 chr19:42007171-42007180 chr19:42007171-42007180

Variant related genes	Relation type
ENSG00000267107	TF binding region
ENSG00000268034	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10406371	0.81[ASN][1000 genomes]
rs10406545	0.81[ASN][1000 genomes]
rs10406988	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10407939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs10410081	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668699	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs11669873	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11672691	0.84[MEX][hapmap]
rs12462897	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap]
rs12973063	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs2191139	0.82[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs3826716	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap]
rs4802119	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4802122	0.87[GIH][hapmap]
rs4803475	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803476	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7248215	0.83[AMR][1000 genomes]
rs7248492	0.92[ASN][1000 genomes]
rs7255742	0.85[GIH][hapmap]
rs8112363	0.82[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061157	chr19:41962486-42007875	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1066225	chr19:41968797-42007875	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	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
7	esv3376048	chr19:41969544-42022873	Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3497342	chr19:41969692-42023108	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3497343	chr19:41969692-42023108	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	esv3319145	chr19:41971761-42025822	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3319144	chr19:41971770-42026041	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3318546	chr19:41972494-42008328	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	esv3318547	chr19:41972494-42008328	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1062563	chr19:41976648-42007875	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1060959	chr19:41976648-42023361	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1057764	chr19:41976648-42023588	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv2760512	chr19:41976660-42023600	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1057852	chr19:41983993-42007875	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv521657	chr19:41984128-42020112	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	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
21	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
22	nsv579601	chr19:42006714-42031592	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7249258	SLC1A5	cis	parietal	SCAN
rs7249258	AC011526.1	cis	Esophagus Muscularis	GTEx
rs7249258	CEACAM21	cis	lymphoblastoid	seeQTL
rs7249258	AC011526.1	cis	Adipose Subcutaneous	GTEx
rs7249258	CEACAM21	cis	multi-tissue	Pritchard
rs7249258	SYMPK	cis	cerebellum	SCAN
rs7249258	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs7249258	FLT3LG	cis	cerebellum	SCAN
rs7249258	APOC1	cis	parietal	SCAN
rs7249258	IRF3	cis	cerebellum	SCAN
rs7249258	SPHK2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42006600-42008200	Flanking Active TSS	A549	lung
2	chr19:42006800-42008000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr19:42007200-42008000	Bivalent Enhancer	Adipose Nuclei	Adipose
4	chr19:42007800-42008000	Enhancers	HUVEC	blood vessel

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