Variant report

Variant	rs892117
Chromosome Location	chr19:40711333-40711334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40696418..40698830-chr19:40709554..40711978,2	K562	blood:

Variant related genes	Relation type
ENSG00000130758	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10423675	0.90[ASN][1000 genomes]
rs11083554	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12151335	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12460555	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12609014	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16974196	0.82[JPT][hapmap]
rs2304186	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs2368575	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs33933140	0.85[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs34894858	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3745195	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3746006	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4490097	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4502340	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4802076	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4803317	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55710849	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67322193	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259541	0.86[JPT][hapmap]
rs7507651	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs8107448	1.00[YRI][hapmap]
rs890773	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv911698	chr19:40689580-40725304	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv911700	chr19:40695598-40725304	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs892117	ZNF404	cis	parietal	SCAN
rs892117	VASP	cis	cerebellum	SCAN
rs892117	DMRTC2	cis	parietal	SCAN
rs892117	CEACAM7	cis	cerebellum	SCAN
rs892117	MAP3K10	cis	Skin Sun Exposed Lower leg	GTEx
rs892117	PLAUR	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40698000-40711400	Weak transcription	Fetal Kidney	kidney
2	chr19:40698400-40714600	Weak transcription	Small Intestine	intestine
3	chr19:40698400-40715400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:40698600-40721200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:40698800-40715600	Weak transcription	Liver	Liver
6	chr19:40698800-40719600	Weak transcription	HSMM	muscle
7	chr19:40698800-40720200	Weak transcription	NHEK	skin
8	chr19:40698800-40721400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:40698800-40722000	Weak transcription	Fetal Thymus	thymus
10	chr19:40699000-40716600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:40699000-40716600	Weak transcription	A549	lung
12	chr19:40699000-40720400	Weak transcription	Psoas Muscle	Psoas
13	chr19:40699000-40722200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr19:40699000-40722200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:40699000-40722400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:40699200-40716800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:40699200-40716800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:40699200-40720200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:40699200-40720400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr19:40699200-40721200	Weak transcription	NH-A	brain
21	chr19:40699200-40721400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:40699400-40716400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:40699400-40721200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr19:40699600-40722000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:40699600-40722200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:40699800-40720000	Weak transcription	NHDF-Ad	bronchial
27	chr19:40699800-40720600	Weak transcription	HepG2	liver
28	chr19:40703000-40713200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:40703200-40713000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:40704000-40712200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:40706800-40712400	Strong transcription	Left Ventricle	heart
32	chr19:40706800-40716800	Weak transcription	GM12878-XiMat	blood
33	chr19:40707000-40716600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:40707000-40722400	Weak transcription	HMEC	breast
35	chr19:40707400-40712600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:40707400-40712600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:40707400-40713000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:40708000-40712200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:40708000-40712800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:40708200-40711800	Strong transcription	Colon Smooth Muscle	Colon
41	chr19:40708200-40712200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:40708200-40712400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:40708200-40713000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:40708600-40711400	Strong transcription	Brain Substantia Nigra	brain
45	chr19:40708600-40711600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:40708600-40711800	Strong transcription	Pancreas	Pancrea
47	chr19:40708600-40712200	Strong transcription	Aorta	Aorta
48	chr19:40708600-40712200	Strong transcription	Spleen	Spleen
49	chr19:40708600-40712400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:40708600-40712600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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