Variant report

Variant	rs10419073
Chromosome Location	chr19:19929654-19929655
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: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10401290	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10401847	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10401908	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10402267	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405029	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406942	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10407581	1.00[EUR][1000 genomes]
rs10408499	0.85[AMR][1000 genomes]
rs10408890	1.00[EUR][1000 genomes]
rs10409568	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411668	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412298	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414667	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416020	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423312	1.00[EUR][1000 genomes]
rs10423574	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423992	1.00[EUR][1000 genomes]
rs10425214	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878325	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879946	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880495	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880971	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880972	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880975	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881233	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881507	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882779	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882889	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346878	1.00[EUR][1000 genomes]
rs16996376	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437283	1.00[EUR][1000 genomes]
rs28622316	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655627	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668259	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28696819	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28698719	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45447205	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55870166	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56413930	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57018770	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57405289	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57691007	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59586774	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60287284	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250673	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251735	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73526738	1.00[EUR][1000 genomes]
rs73526768	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73528913	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73528956	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73923028	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73925538	1.00[EUR][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

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
2	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
9	chr19:19909200-19931600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:19914400-19931400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:19914400-19931600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:19915800-19930400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:19916200-19931200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
14	chr19:19916800-19931600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:19917000-19931400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr19:19917000-19931600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:19919200-19931200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr19:19920200-19931200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:19920600-19931200	Weak transcription	Right Atrium	heart
20	chr19:19922000-19931200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:19922200-19931600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:19922600-19931600	Weak transcription	Ovary	ovary
23	chr19:19923200-19931600	Weak transcription	Pancreas	Pancrea
24	chr19:19923600-19931600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:19923800-19931600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:19924200-19931600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:19924400-19931400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:19924400-19931400	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr19:19924400-19933200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:19925800-19931600	Weak transcription	HSMM	muscle
31	chr19:19926200-19931400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr19:19926400-19931600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr19:19926600-19930800	Weak transcription	Right Ventricle	heart
34	chr19:19926600-19931400	Weak transcription	Placenta	Placenta
35	chr19:19926600-19931600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:19926800-19929800	Weak transcription	Fetal Brain Female	brain
37	chr19:19926800-19929800	Weak transcription	Osteobl	bone
38	chr19:19927200-19929800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:19927800-19930200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19927800-19930400	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr19:19927800-19930400	ZNF genes & repeats	Liver	Liver
42	chr19:19927800-19931200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:19927800-19931200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr19:19928000-19930400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:19928000-19936600	ZNF genes & repeats	GM12878-XiMat	blood
46	chr19:19928200-19930600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:19928200-19931600	Weak transcription	Aorta	Aorta
48	chr19:19928400-19930400	ZNF genes & repeats	Fetal Thymus	thymus
49	chr19:19928400-19931000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr19:19928400-19931000	Weak transcription	Brain Cingulate Gyrus	brain

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