Variant report

Variant	rs7253234
Chromosome Location	chr19:55962857-55962858
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55961478..55964648-chr19:56109795..56113001,3	K562	blood:
2	chr19:55590562..55592991-chr19:55962507..55964456,2	K562	blood:
3	chr19:55960899..55962877-chr19:55970190..55972301,2	MCF-7	breast:
4	chr19:55915948..55921315-chr19:55958410..55968133,14	K562	blood:
5	chr19:55961478..55964648-chr19:56109524..56113001,4	K562	blood:
6	chr19:55917232..55920888-chr19:55959942..55966428,7	K562	blood:
7	chr19:55895254..55899821-chr19:55961359..55968155,8	K562	blood:
8	chr19:55962707..55966415-chr19:56152837..56156064,3	K562	blood:
9	chr19:55962141..55964199-chr19:55986076..55988718,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108106	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000171425	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10412033	0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12462602	0.93[ASN][1000 genomes]
rs2303089	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs62128233	0.93[ASN][1000 genomes]
rs7247719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
2	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
4	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv912477	chr19:55936376-55972950	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv912478	chr19:55936376-56045522	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv912479	chr19:55942456-55969746	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55960600-55966600	Weak transcription	Pancreas	Pancrea
2	chr19:55960800-55963800	Active TSS	Brain Anterior Caudate	brain
3	chr19:55960800-55964600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr19:55961200-55963000	Weak transcription	Gastric	stomach
5	chr19:55961200-55963200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:55961200-55964000	Bivalent/Poised TSS	Fetal Brain Female	brain
7	chr19:55961800-55965000	Active TSS	Brain Angular Gyrus	brain
8	chr19:55962000-55964000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
9	chr19:55962200-55963000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr19:55962200-55964600	Active TSS	Brain Cingulate Gyrus	brain
11	chr19:55962400-55963000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:55962400-55963000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:55962400-55963000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:55962400-55963000	Bivalent/Poised TSS	Thymus	Thymus
15	chr19:55962400-55963200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:55962400-55964600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr19:55962600-55963000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:55962600-55963000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:55962600-55963000	Active TSS	Right Ventricle	heart
20	chr19:55962600-55963000	Bivalent/Poised TSS	A549	lung
21	chr19:55962600-55963000	Bivalent/Poised TSS	Dnd41	blood
22	chr19:55962600-55963600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr19:55962600-55963600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
24	chr19:55962600-55963800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:55962600-55963800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:55962600-55964000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr19:55962600-55964200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:55962600-55964800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr19:55962800-55963000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:55962800-55963000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:55962800-55963000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
32	chr19:55962800-55963000	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
33	chr19:55962800-55963000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr19:55962800-55963000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:55962800-55963000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:55962800-55963000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:55962800-55963000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:55962800-55963000	Bivalent Enhancer	Colonic Mucosa	Colon
39	chr19:55962800-55963000	Active TSS	Ovary	ovary
40	chr19:55962800-55963000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
41	chr19:55962800-55963000	Bivalent Enhancer	HMEC	breast
42	chr19:55962800-55963200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:55962800-55963200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
44	chr19:55962800-55963200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:55962800-55963200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:55962800-55963200	Active TSS	HepG2	liver
47	chr19:55962800-55963400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:55962800-55963600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:55962800-55963600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr19:55962800-55963600	Active TSS	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links