Variant report

Variant	rs870204
Chromosome Location	chr10:45458485-45458486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr10:45458376-45459207	HEK293-T-REx	kidney:	n/a	chr10:45458627-45458636 chr10:45458650-45458671
2	POLR2A	chr10:45457577-45464667	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:45458313-45459329	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:45458224-45466240	HepG2	liver:	n/a	n/a
5	POLR2A	chr10:45458474-45458611	HepG2	liver:	n/a	n/a
6	RCOR1	chr10:45458474-45460045	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:45458411-45459268	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45452754..45457463-chr10:45457605..45460897,6	MCF-7	breast:
2	chr10:45453822..45456715-chr10:45457223..45459708,3	MCF-7	breast:
3	chr10:45453904..45457174-chr10:45457388..45460255,4	K562	blood:
4	chr10:45443748..45446726-chr10:45456991..45458960,2	MCF-7	breast:

Variant related genes	Relation type
TMEM72-AS1	TF binding region
ENSG00000273363	TF binding region
ENSG00000273363	Chromatin interaction
ENSG00000224812	Chromatin interaction
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10793573	0.81[ASN][1000 genomes]
rs11595676	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12263146	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2183993	0.85[CEU][hapmap]
rs59626742	0.99[EUR][1000 genomes]
rs72780655	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72780658	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1035235	chr10:45442303-45467948	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs870204	ZNF488	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45455400-45462800	Flanking Active TSS	GM12878-XiMat	blood
2	chr10:45455600-45459200	Weak transcription	Hela-S3	cervix
3	chr10:45455600-45459400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:45455600-45462600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:45455600-45465200	Enhancers	Fetal Thymus	thymus
6	chr10:45455600-45465200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr10:45455800-45458800	Weak transcription	Fetal Brain Male	brain
8	chr10:45455800-45459400	Weak transcription	HMEC	breast
9	chr10:45455800-45459600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:45455800-45460600	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr10:45455800-45461400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:45455800-45463200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:45455800-45464000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:45455800-45465600	Weak transcription	Ovary	ovary
15	chr10:45456000-45458600	Weak transcription	Dnd41	blood
16	chr10:45456000-45458600	Weak transcription	NH-A	brain
17	chr10:45456000-45459000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:45456000-45459200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:45456000-45459200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:45456000-45459600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:45456000-45459800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:45456000-45460800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:45456000-45463000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr10:45456000-45463400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:45456200-45458600	Weak transcription	Lung	lung
26	chr10:45456200-45458800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:45456200-45459400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr10:45456200-45459400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr10:45456200-45459400	Weak transcription	NHLF	lung
30	chr10:45456200-45459600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr10:45456200-45460200	Flanking Active TSS	HepG2	liver
32	chr10:45456200-45463200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:45456200-45463600	Weak transcription	Esophagus	oesophagus
34	chr10:45456200-45465000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:45456400-45458600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:45456400-45458800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:45456400-45459600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:45456400-45459800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr10:45456400-45461600	Weak transcription	Osteobl	bone
40	chr10:45456400-45466200	Weak transcription	Aorta	Aorta
41	chr10:45456600-45459000	Weak transcription	Fetal Brain Female	brain
42	chr10:45456600-45459000	Weak transcription	Stomach Mucosa	stomach
43	chr10:45456600-45461400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr10:45456600-45461600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr10:45456600-45461800	Weak transcription	HUVEC	blood vessel
46	chr10:45456600-45462800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr10:45456800-45458600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr10:45456800-45458600	Weak transcription	Brain Germinal Matrix	brain
49	chr10:45456800-45458800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr10:45456800-45458800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links