Variant report

Variant	rs12972895
Chromosome Location	chr19:38925353-38925354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38879240..38881217-chr19:38924202..38926113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188766	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11883126	1.00[EUR][1000 genomes]
rs12971920	1.00[EUR][1000 genomes]
rs12972609	1.00[EUR][1000 genomes]
rs12973210	1.00[EUR][1000 genomes]
rs12974363	1.00[EUR][1000 genomes]
rs12974979	1.00[EUR][1000 genomes]
rs12975212	0.96[EUR][1000 genomes]
rs12982894	1.00[EUR][1000 genomes]
rs12986359	1.00[EUR][1000 genomes]
rs17640544	1.00[EUR][1000 genomes]
rs34026587	1.00[EUR][1000 genomes]
rs34158728	1.00[EUR][1000 genomes]
rs34377632	1.00[EUR][1000 genomes]
rs34456672	1.00[EUR][1000 genomes]
rs35136248	1.00[EUR][1000 genomes]
rs71356804	1.00[EUR][1000 genomes]
rs71356805	1.00[EUR][1000 genomes]
rs9916978	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1055309	chr19:38896244-38945851	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1065803	chr19:38903099-38945851	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv1066138	chr19:38904072-38949729	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38923800-38926000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38923800-38926200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:38924000-38925400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
4	chr19:38924000-38925400	Bivalent Enhancer	A549	lung
5	chr19:38924000-38925600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:38924000-38925600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:38924000-38925600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr19:38924000-38925800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
9	chr19:38924000-38926400	Active TSS	HSMMtube	muscle
10	chr19:38924200-38925600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:38924200-38925600	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:38924200-38925800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:38924200-38926000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
14	chr19:38924200-38926000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
15	chr19:38924200-38927400	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr19:38924400-38925400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:38924400-38925600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:38924400-38925800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr19:38924400-38925800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr19:38924400-38925800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
21	chr19:38924600-38925400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:38924600-38925400	Weak transcription	Right Atrium	heart
23	chr19:38924600-38925600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr19:38924600-38925600	Enhancers	Spleen	Spleen
25	chr19:38924600-38925800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:38924600-38925800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:38924600-38926000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr19:38924600-38926000	Flanking Active TSS	K562	blood
29	chr19:38924800-38925400	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:38924800-38925400	Bivalent/Poised TSS	Placenta	Placenta
31	chr19:38924800-38925600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:38924800-38925600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
33	chr19:38925000-38925400	Active TSS	Brain Substantia Nigra	brain
34	chr19:38925000-38925600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr19:38925000-38925800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr19:38925000-38925800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:38925000-38926000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr19:38925000-38926000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
39	chr19:38925000-38926200	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:38925200-38925400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38925200-38925400	Active TSS	HSMM	muscle
42	chr19:38925200-38925600	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr19:38925200-38925600	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:38925200-38925600	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr19:38925200-38925600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:38925200-38925800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:38925200-38925800	Flanking Active TSS	Psoas Muscle	Psoas
48	chr19:38925200-38926000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr19:38925200-38926400	Flanking Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links