Variant report

Variant	rs10404296
Chromosome Location	chr19:19927693-19927694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19927559..19930020-chr19:19975379..19977771,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256771	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10412885	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11085278	0.81[AFR][1000 genomes]
rs12710110	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12975051	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12977036	0.84[AFR][1000 genomes]
rs16996360	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248930	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248931	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248932	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248933	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248934	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248942	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248944	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248945	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248946	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248947	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248948	0.88[ASN][1000 genomes]
rs248949	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248951	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248952	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248954	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3087767	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762190	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808216	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808989	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808991	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808995	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808998	0.95[AFR][1000 genomes]
rs6511050	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7246727	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248808	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256535	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8106100	0.81[EUR][1000 genomes]
rs8109240	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111421	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10404296	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs10404296	ZNF682	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 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	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine
9	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
11	chr19:19909200-19931600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:19914400-19927800	Weak transcription	Aorta	Aorta
13	chr19:19914400-19929600	Weak transcription	HSMMtube	muscle
14	chr19:19914400-19931400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:19914400-19931600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:19915200-19929600	Weak transcription	NHLF	lung
17	chr19:19915800-19930400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:19916200-19931200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr19:19916800-19931600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:19917000-19929400	Weak transcription	Fetal Brain Male	brain
21	chr19:19917000-19931400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:19917000-19931600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:19919200-19931200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:19920200-19931200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr19:19920600-19931200	Weak transcription	Right Atrium	heart
26	chr19:19921200-19929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:19922000-19931200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:19922200-19931600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:19922600-19929400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr19:19922600-19931600	Weak transcription	Ovary	ovary
31	chr19:19923200-19931600	Weak transcription	Pancreas	Pancrea
32	chr19:19923600-19928000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:19923600-19931600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:19923800-19931600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:19924200-19931600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:19924400-19928000	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:19924400-19928800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19924400-19931400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:19924400-19931400	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr19:19924400-19933200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:19925400-19927800	Genic enhancers	Dnd41	blood
42	chr19:19925600-19928200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:19925600-19929400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr19:19925600-19929600	Weak transcription	NHDF-Ad	bronchial
45	chr19:19925800-19928000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:19925800-19931600	Weak transcription	HSMM	muscle
47	chr19:19926000-19928600	Enhancers	Brain Substantia Nigra	brain
48	chr19:19926200-19931400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr19:19926400-19929200	Weak transcription	Fetal Kidney	kidney
50	chr19:19926400-19929400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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