Variant report

Variant	rs3890526
Chromosome Location	chr19:40405436-40405437
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10853730	0.89[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1814278	0.80[EUR][1000 genomes]
rs1814279	0.80[EUR][1000 genomes]
rs28540820	0.80[EUR][1000 genomes]
rs3746013	0.81[JPT][hapmap]
rs3859559	0.81[EUR][1000 genomes]
rs4802064	0.80[EUR][1000 genomes]
rs4803311	0.95[CEU][hapmap];0.87[YRI][hapmap]
rs741143	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv2483	chr19:40340641-40435505	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv482218	chr19:40353963-40440533	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1846009	chr19:40353983-40410533	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1066339	chr19:40357018-40427903	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv12245	chr19:40362630-40411824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv961218	chr19:40365009-40412126	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1847508	chr19:40365173-40406611	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1823796	chr19:40365173-40415061	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1828434	chr19:40367739-40409877	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv1819299	chr19:40367739-40412951	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	esv1847388	chr19:40367831-40408856	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv1819359	chr19:40367831-40413151	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv1800571	chr19:40385437-40408910	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv3325321	chr19:40390872-40406938	Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3890526	CEACAM4	cis	cerebellum	SCAN
rs3890526	FCGBP	cis	Whole Blood	GTEx
rs3890526	ZNF229	cis	parietal	SCAN
rs3890526	BLOC1S3	cis	cerebellum	SCAN
rs3890526	LYPD5	cis	cerebellum	SCAN
rs3890526	NANOS2	cis	cerebellum	SCAN
rs3890526	STRN4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40399200-40411800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40400200-40410600	Weak transcription	Fetal Stomach	stomach
3	chr19:40402000-40419600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:40402800-40406000	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:40404000-40406000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:40404200-40410600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:40404400-40412000	Weak transcription	Colonic Mucosa	Colon
8	chr19:40404600-40405600	Weak transcription	Fetal Thymus	thymus
9	chr19:40404600-40407600	Weak transcription	Primary T cells from cord blood	blood
10	chr19:40404600-40408000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr19:40404600-40409000	Weak transcription	HepG2	liver
12	chr19:40404600-40412800	Weak transcription	A549	lung
13	chr19:40404600-40414800	Weak transcription	Stomach Mucosa	stomach
14	chr19:40404600-40421000	Weak transcription	Fetal Intestine Small	intestine
15	chr19:40404800-40419600	Weak transcription	Fetal Intestine Large	intestine
16	chr19:40404800-40429600	Weak transcription	Primary B cells from cord blood	blood
17	chr19:40405200-40413200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr19:40405400-40405600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
19	chr19:40405400-40405800	Bivalent Enhancer	NHEK	skin

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