Variant report

Variant	rs7246983
Chromosome Location	chr19:19904510-19904511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10407920	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412409	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419635	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854013	0.93[ASN][1000 genomes]
rs11878280	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461018	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12973032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975121	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2335360	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs23654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248938	0.80[EUR][1000 genomes]
rs248939	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs248940	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs248941	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs248955	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878398	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34277739	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35018071	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280091	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808989	0.83[CEU][hapmap]
rs4990741	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60041535	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252985	0.88[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104136	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8108416	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111421	0.88[CEU][hapmap]
rs919785	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

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	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	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7246983	CHERP	cis	cerebellum	SCAN
rs7246983	GLT25D1	cis	parietal	SCAN
rs7246983	ZNF253	cis	lymphoblastoid	seeQTL
rs7246983	USHBP1	cis	cerebellum	SCAN
rs7246983	ELL	cis	parietal	SCAN
rs7246983	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs7246983	LRRC25	cis	parietal	SCAN

Chromatin state (count:117 , 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	chr19:19888600-19906400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr19:19888600-19906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:19888600-19909000	Weak transcription	K562	blood
5	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
6	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
7	chr19:19889600-19904600	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:19895400-19908200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:19895600-19907200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr19:19895600-19909000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:19895600-19909000	ZNF genes & repeats	Liver	Liver
15	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
17	chr19:19895800-19908200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:19895800-19914800	Strong transcription	Dnd41	blood
19	chr19:19896000-19909200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:19896600-19905400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:19896600-19905800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:19896800-19908000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:19897200-19904600	Strong transcription	Osteobl	bone
24	chr19:19897200-19905800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:19897200-19906600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:19897200-19907200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:19897200-19908600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
28	chr19:19897200-19918600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:19897400-19907600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr19:19898400-19904600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr19:19899400-19904800	Strong transcription	HSMM	muscle
32	chr19:19899600-19907000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr19:19900000-19915200	Weak transcription	HepG2	liver
34	chr19:19900800-19905800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:19900800-19908200	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr19:19901000-19909000	ZNF genes & repeats	GM12878-XiMat	blood
37	chr19:19902000-19905400	ZNF genes & repeats	NHDF-Ad	bronchial
38	chr19:19902000-19914400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:19902200-19904600	Weak transcription	NHLF	lung
40	chr19:19902400-19904600	Weak transcription	Stomach Mucosa	stomach
41	chr19:19902600-19904600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:19902600-19904600	Weak transcription	Thymus	Thymus
43	chr19:19902600-19904800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:19902600-19904800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:19902600-19905400	Weak transcription	Brain Anterior Caudate	brain
46	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
47	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr19:19902800-19910200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:19903000-19904600	Weak transcription	Brain Substantia Nigra	brain
50	chr19:19903000-19904600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links