Variant report

Variant	rs4808993
Chromosome Location	chr19:19920967-19920968
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11085277	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12327770	0.90[ASN][1000 genomes]
rs16996320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808992	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72620573	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72620574	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72620575	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737195	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
7	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv578799	chr19:19901136-19967970	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
12	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4808993	ZNF682	cis	parietal	SCAN
rs4808993	SUGP2	cis	cerebellum	SCAN
rs4808993	ZNF682	cis	Muscle Skeletal	GTEx
rs4808993	ZNF253	Cis_1M	lymphoblastoid	RTeQTL
rs4808993	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs4808993	ZNF253	cis	parietal	SCAN
rs4808993	ZNF253	cis	Nerve Tibial	GTEx
rs4808993	ZNF506	cis	Heart Left Ventricle	GTEx
rs4808993	ZNF682	cis	cerebellum	SCAN
rs4808993	LRRC25	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
2	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
3	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
5	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:19907000-19923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine
12	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
14	chr19:19909200-19931600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:19912400-19921600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:19914200-19924600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:19914200-19926200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:19914400-19921200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:19914400-19922200	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:19914400-19922400	Weak transcription	Left Ventricle	heart
21	chr19:19914400-19922400	Weak transcription	Ovary	ovary
22	chr19:19914400-19922400	Weak transcription	Pancreas	Pancrea
23	chr19:19914400-19922400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:19914400-19922600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:19914400-19924600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:19914400-19925400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:19914400-19926000	Weak transcription	Brain Substantia Nigra	brain
28	chr19:19914400-19926000	Weak transcription	Spleen	Spleen
29	chr19:19914400-19927600	Weak transcription	Gastric	stomach
30	chr19:19914400-19927800	Weak transcription	Aorta	Aorta
31	chr19:19914400-19929600	Weak transcription	HSMMtube	muscle
32	chr19:19914400-19931400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:19914400-19931600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:19914600-19923200	Weak transcription	Colonic Mucosa	Colon
35	chr19:19914600-19925600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:19914800-19924600	Weak transcription	Fetal Brain Female	brain
37	chr19:19914800-19925400	Weak transcription	NH-A	brain
38	chr19:19915200-19929600	Weak transcription	NHLF	lung
39	chr19:19915800-19923200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19915800-19926800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:19915800-19930400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:19916200-19931200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
43	chr19:19916400-19921200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:19916600-19921200	Strong transcription	Dnd41	blood
45	chr19:19916800-19922000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr19:19916800-19931600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr19:19917000-19921600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:19917000-19923000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:19917000-19923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr19:19917000-19923200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links