Variant report

Variant	rs3745938
Chromosome Location	chr19:42071167-42071168
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10406221	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs10409976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415465	0.99[ASN][1000 genomes]
rs10415860	0.99[ASN][1000 genomes]
rs10421584	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10421785	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11083627	0.86[JPT][hapmap]
rs12150975	0.85[JPT][hapmap]
rs12709854	0.97[ASN][1000 genomes]
rs12709855	0.97[ASN][1000 genomes]
rs12983999	0.86[JPT][hapmap]
rs17724225	0.97[ASN][1000 genomes]
rs28433747	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28709791	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34007391	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35834169	0.96[ASN][1000 genomes]
rs3745936	0.83[CHB][hapmap]
rs4803481	0.86[JPT][hapmap]
rs57979746	0.94[ASN][1000 genomes]
rs58163879	0.86[ASN][1000 genomes]
rs60646575	0.91[ASN][1000 genomes]
rs714106	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs7247842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251994	0.91[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7257657	0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.91[ASN][1000 genomes]
rs740591	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs758350	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3745938	R29124_1	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 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	chr19:42069600-42071200	Bivalent Enhancer	Liver	Liver
4	chr19:42069600-42071200	Enhancers	Lung	lung
5	chr19:42069600-42071200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
6	chr19:42069600-42071200	Bivalent Enhancer	HUVEC	blood vessel
7	chr19:42069600-42071400	Bivalent Enhancer	Colonic Mucosa	Colon
8	chr19:42069600-42071400	Bivalent Enhancer	Left Ventricle	heart
9	chr19:42069600-42071600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:42069600-42071800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
11	chr19:42069600-42071800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr19:42069600-42071800	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr19:42069600-42071800	Enhancers	Spleen	Spleen
14	chr19:42069600-42072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:42069600-42073000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42069800-42071200	Enhancers	Gastric	stomach
17	chr19:42069800-42071600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr19:42070000-42071400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:42070000-42071400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:42070000-42071400	Bivalent Enhancer	Fetal Thymus	thymus
21	chr19:42070000-42071800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
22	chr19:42070000-42071800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
23	chr19:42070000-42071800	Bivalent Enhancer	Fetal Intestine Small	intestine
24	chr19:42070000-42072000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr19:42070200-42071200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr19:42070400-42071400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
27	chr19:42070400-42071600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:42070800-42071200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:42070800-42071200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:42070800-42071200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:42070800-42071200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:42070800-42071200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
33	chr19:42070800-42071200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
34	chr19:42070800-42071200	Flanking Active TSS	Right Atrium	heart
35	chr19:42070800-42071400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:42070800-42071400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
37	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
39	chr19:42070800-42071400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
41	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr19:42070800-42071400	Bivalent Enhancer	Fetal Brain Male	brain
43	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
44	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	A549	lung
45	chr19:42070800-42071400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr19:42070800-42071600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr19:42070800-42071600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr19:42070800-42071600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr19:42070800-42071600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:42070800-42071600	Flanking Active TSS	Primary hematopoietic stem cells	blood

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