Variant report

Variant	rs4141218
Chromosome Location	chr19:42081907-42081908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10420470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076362	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11882144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476769	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476770	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745936	0.82[CEU][hapmap]
rs3745937	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4578777	1.00[ASN][1000 genomes]
rs4803480	0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs723902	1.00[ASN][1000 genomes]
rs7255679	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs758349	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110782	1.00[JPT][hapmap]
rs9304595	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1057624	chr19:42057334-42152828	Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv960930	chr19:42080172-42093112	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4141218	CNFN	cis	cerebellum	SCAN
rs4141218	CEACAM21	cis	lung	GTEx
rs4141218	CEACAM21	cis	lymphoblastoid	seeQTL
rs4141218	R29124_1	cis	multi-tissue	Pritchard
rs4141218	CEACAMP3	cis	Whole Blood	GTEx
rs4141218	CEACAMP3	cis	lung	GTEx
rs4141218	SPHK2	cis	cerebellum	SCAN
rs4141218	CEACAM21	cis	Whole Blood	GTEx
rs4141218	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs4141218	TMEM143	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42071600-42082000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:42077200-42082000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:42077400-42082000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr19:42077400-42082000	Weak transcription	Lung	lung
5	chr19:42077600-42082000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:42077600-42082000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:42079800-42082000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:42079800-42082200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:42080000-42082000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:42080200-42082000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:42080400-42082000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:42081600-42082200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr19:42081600-42083000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:42081800-42082000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr19:42081800-42082200	Bivalent Enhancer	Adipose Nuclei	Adipose
16	chr19:42081800-42082200	Enhancers	Spleen	Spleen
17	chr19:42081800-42082200	Enhancers	GM12878-XiMat	blood
18	chr19:42081800-42082400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr19:42081800-42082400	Enhancers	Primary B cells from cord blood	blood
20	chr19:42081800-42082400	Enhancers	Primary T cells from cord blood	blood
21	chr19:42081800-42082400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr19:42081800-42082400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:42081800-42082400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:42081800-42082400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr19:42081800-42082400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr19:42081800-42082400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:42081800-42082600	Enhancers	Primary B cells from peripheral blood	blood
28	chr19:42081800-42082600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:42081800-42082600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr19:42081800-42082800	Enhancers	Left Ventricle	heart
31	chr19:42081800-42083200	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links