Variant report

Variant	rs7248808
Chromosome Location	chr19:19923100-19923101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10404296	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10412885	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710110	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs16996360	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248930	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248931	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248932	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248933	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248934	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248936	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs248942	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248948	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248949	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248951	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248952	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248954	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762190	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808216	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808989	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808995	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246727	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256535	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106100	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109240	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111421	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7248808	ATP13A1	cis	parietal	SCAN
rs7248808	OR4C6	trans	parietal	SCAN
rs7248808	LINC00663	cis	Artery Tibial	GTEx
rs7248808	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs7248808	ZNF682	cis	Muscle Skeletal	GTEx
rs7248808	ZNF93	cis	cerebellum	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	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:19907000-19923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine
11	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
13	chr19:19909200-19931600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:19914200-19924600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:19914200-19926200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:19914400-19924600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:19914400-19925400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:19914400-19926000	Weak transcription	Brain Substantia Nigra	brain
19	chr19:19914400-19926000	Weak transcription	Spleen	Spleen
20	chr19:19914400-19927600	Weak transcription	Gastric	stomach
21	chr19:19914400-19927800	Weak transcription	Aorta	Aorta
22	chr19:19914400-19929600	Weak transcription	HSMMtube	muscle
23	chr19:19914400-19931400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:19914400-19931600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:19914600-19923200	Weak transcription	Colonic Mucosa	Colon
26	chr19:19914600-19925600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:19914800-19924600	Weak transcription	Fetal Brain Female	brain
28	chr19:19914800-19925400	Weak transcription	NH-A	brain
29	chr19:19915200-19929600	Weak transcription	NHLF	lung
30	chr19:19915800-19923200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:19915800-19926800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr19:19915800-19930400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:19916200-19931200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
34	chr19:19916800-19931600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:19917000-19923200	Weak transcription	NHDF-Ad	bronchial
36	chr19:19917000-19924400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:19917000-19924800	Weak transcription	HSMM	muscle
38	chr19:19917000-19929400	Weak transcription	Fetal Brain Male	brain
39	chr19:19917000-19931400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:19917000-19931600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:19917200-19924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:19917400-19924400	Weak transcription	Esophagus	oesophagus
43	chr19:19917400-19924400	Weak transcription	Thymus	Thymus
44	chr19:19917400-19924600	Weak transcription	Osteobl	bone
45	chr19:19917600-19926200	Weak transcription	Placenta	Placenta
46	chr19:19918000-19925400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:19919200-19923200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:19919200-19931200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr19:19919800-19924600	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr19:19920000-19923600	ZNF genes & repeats	Primary B cells from cord blood	blood

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