Variant report

Variant	rs2282305
Chromosome Location	chr10:97421345-97421346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:97420761-97422271	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr10:97421183-97422525	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:97419292..97421837-chr10:97434385..97436890,2	K562	blood:
2	chr10:97419292..97421697-chr10:97434103..97436890,2	K562	blood:
3	chr10:97403502..97406467-chr10:97420459..97422699,2	K562	blood:
4	chr10:97420551..97423519-chr10:97425006..97428987,4	MCF-7	breast:
5	chr10:97415703..97418525-chr10:97420454..97423040,3	MCF-7	breast:

No data

Variant related genes	Relation type
ALDH18A1	TF binding region
ENSG00000059573	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10882654	0.89[JPT][hapmap]
rs11188410	0.88[JPT][hapmap]
rs11188412	0.88[JPT][hapmap]
rs11188415	0.88[JPT][hapmap]
rs11188418	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11188419	0.88[JPT][hapmap]
rs11188423	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188428	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11188431	0.88[JPT][hapmap]
rs11188433	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11188466	0.88[JPT][hapmap]
rs11188469	0.88[JPT][hapmap]
rs11188475	0.88[JPT][hapmap]
rs11188502	1.00[JPT][hapmap]
rs11553577	0.88[JPT][hapmap]
rs12358517	0.88[JPT][hapmap]
rs12784530	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3181121	0.88[JPT][hapmap];0.81[MKK][hapmap]
rs35722210	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3818833	0.88[JPT][hapmap]
rs7073937	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7080192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7090630	0.88[JPT][hapmap]
rs7093453	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2282305	ZFYVE27	cis	parietal	SCAN
rs2282305	ALDH18A1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97416600-97441000	Weak transcription	Spleen	Spleen
2	chr10:97416800-97421600	Weak transcription	Gastric	stomach
3	chr10:97416800-97423000	Weak transcription	Lung	lung
4	chr10:97416800-97423000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:97416800-97441600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:97416800-97442400	Weak transcription	Small Intestine	intestine
7	chr10:97416800-97443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:97417000-97421600	Weak transcription	A549	lung
9	chr10:97417000-97422000	Weak transcription	Fetal Stomach	stomach
10	chr10:97417000-97422200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr10:97417000-97422800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:97417000-97422800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:97417000-97422800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:97417000-97422800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:97417000-97422800	Weak transcription	Fetal Brain Female	brain
16	chr10:97417000-97422800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:97417000-97423000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:97417000-97423000	Weak transcription	Primary T cells from cord blood	blood
19	chr10:97417000-97423000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:97417000-97423000	Weak transcription	Pancreas	Pancrea
21	chr10:97417000-97423200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:97417000-97423200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr10:97417000-97423200	Weak transcription	Left Ventricle	heart
24	chr10:97417000-97423400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:97417000-97423400	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:97417000-97423800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:97417000-97424000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:97417000-97428600	Weak transcription	Fetal Kidney	kidney
29	chr10:97417000-97434800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr10:97417000-97434800	Weak transcription	Ovary	ovary
31	chr10:97417000-97434800	Weak transcription	HUVEC	blood vessel
32	chr10:97417000-97436200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr10:97417000-97436400	Weak transcription	HMEC	breast
34	chr10:97417000-97437400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr10:97417000-97439800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:97417000-97439800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr10:97417000-97439800	Weak transcription	Brain Substantia Nigra	brain
38	chr10:97417000-97441000	Weak transcription	HSMMtube	muscle
39	chr10:97417000-97442400	Weak transcription	Aorta	Aorta
40	chr10:97417000-97444200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:97417000-97445200	Weak transcription	Colonic Mucosa	Colon
42	chr10:97417000-97445800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr10:97417000-97445800	Weak transcription	NHLF	lung
44	chr10:97417200-97421600	Weak transcription	Liver	Liver
45	chr10:97417200-97422400	Weak transcription	Adipose Nuclei	Adipose
46	chr10:97417200-97422800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr10:97417200-97422800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr10:97417200-97422800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr10:97417200-97422800	Weak transcription	Fetal Muscle Leg	muscle
50	chr10:97417200-97423000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links