Variant report

Variant	rs3745937
Chromosome Location	chr19:42071289-42071290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10420470	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1076362	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11882144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1476769	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1476770	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141218	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4578777	0.90[ASN][1000 genomes]
rs4803480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723902	0.90[ASN][1000 genomes]
rs7255679	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs758349	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8110782	1.00[JPT][hapmap]
rs9304595	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	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
4	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
5	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
6	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
7	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3745937	CEACAM21	cis	Adipose Subcutaneous	GTEx
rs3745937	CEACAMP3	cis	lung	GTEx
rs3745937	CEACAMP3	cis	Whole Blood	GTEx
rs3745937	CEACAM21	cis	Whole Blood	GTEx
rs3745937	R29124_1	cis	multi-tissue	Pritchard
rs3745937	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42069400-42071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:42069400-42077600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:42069600-42071400	Bivalent Enhancer	Colonic Mucosa	Colon
4	chr19:42069600-42071400	Bivalent Enhancer	Left Ventricle	heart
5	chr19:42069600-42071600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:42069600-42071800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
7	chr19:42069600-42071800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr19:42069600-42071800	Bivalent Enhancer	Fetal Intestine Large	intestine
9	chr19:42069600-42071800	Enhancers	Spleen	Spleen
10	chr19:42069600-42072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:42069600-42073000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:42069800-42071600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr19:42070000-42071400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr19:42070000-42071400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:42070000-42071400	Bivalent Enhancer	Fetal Thymus	thymus
16	chr19:42070000-42071800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr19:42070000-42071800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
18	chr19:42070000-42071800	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr19:42070000-42072000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr19:42070400-42071400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
21	chr19:42070400-42071600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:42070800-42071400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:42070800-42071400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
26	chr19:42070800-42071400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
28	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr19:42070800-42071400	Bivalent Enhancer	Fetal Brain Male	brain
30	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	A549	lung
32	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr19:42070800-42071600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr19:42070800-42071600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:42070800-42071600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
36	chr19:42070800-42071600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:42070800-42071600	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr19:42070800-42071600	Bivalent/Poised TSS	Thymus	Thymus
39	chr19:42070800-42071800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr19:42070800-42071800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
41	chr19:42070800-42071800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:42070800-42072000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:42071000-42071400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:42071000-42071400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
45	chr19:42071000-42071400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
46	chr19:42071000-42071400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:42071000-42071400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
48	chr19:42071000-42071400	Bivalent Enhancer	Fetal Lung	lung
49	chr19:42071000-42071400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
50	chr19:42071000-42071400	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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