Variant report

Variant	rs10036206
Chromosome Location	chr5:90609178-90609179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:90595038-90610657	U87	brain:	n/a	n/a
2	POLR2A	chr5:90608809-90609446	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:90604813-90609443	U87	brain:	n/a	n/a
4	ESR1	chr5:90609074-90609440	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr5:90606927-90609466	A549	lung:	n/a	n/a
6	TCF12	chr5:90607081-90609494	A549	lung:	n/a	n/a
7	POLR2A	chr5:90596852-90610582	U87	brain:	n/a	n/a
8	POLR2A	chr5:90606580-90610482	Hela-S3	cervix:	n/a	n/a
9	ESR1	chr5:90609095-90609455	ECC-1	luminal epithelium:	n/a	n/a
10	RCOR1	chr5:90608555-90609225	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:90607078-90609477	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr5:90604771-90610527	U87	brain:	n/a	n/a
13	MAX	chr5:90608607-90609452	A549	lung:	n/a	n/a
14	RCOR1	chr5:90607062-90609423	IMR90	lung:	n/a	n/a
15	POLR2A	chr5:90596037-90609349	A549	lung:	n/a	n/a
16	POLR2A	chr5:90606798-90610471	IMR90	lung:	n/a	n/a
17	POLR2A	chr5:90608812-90609443	Hela-S3	cervix:	n/a	n/a
18	GTF2F1	chr5:90609036-90609304	Hela-S3	cervix:	n/a	n/a
19	MAX	chr5:90608993-90609343	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:90608764-90609391	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:90607284..90611861-chr5:90674569..90683045,11	K562	blood:
2	chr5:90575227..90576970-chr5:90607873..90610168,2	K562	blood:
3	chr5:90608430..90610124-chr5:90673476..90676069,2	K562	blood:
4	chr5:90607483..90611926-chr5:90672625..90681906,20	MCF-7	breast:
5	chr5:90608356..90610045-chr5:90671011..90673343,2	K562	blood:
6	chr5:90605667..90612137-chr5:90676262..90681561,13	K562	blood:
7	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
8	chr5:90607535..90610829-chr5:90673824..90679078,6	MCF-7	breast:
9	chr5:90576418..90578111-chr5:90608143..90610210,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARRDC3-1	chr5:90608895-90609354	XLOC_004924
2	lnc-GPR98-2	chr5:90608491-90609286	XLOC_004468

No data

Variant related genes	Relation type
LUCAT1	TF binding region
ENSG00000113369	Chromatin interaction
ENSG00000234292	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10038890	0.84[AFR][1000 genomes]
rs12697808	0.89[AFR][1000 genomes]
rs13176999	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941891	0.84[CHB][hapmap]
rs2941905	0.84[CHB][hapmap]
rs2973463	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7727632	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9293565	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10036206	CCNH	cis	parietal	SCAN
rs10036206	ANKRD32	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90605400-90611200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr5:90605600-90610200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:90605800-90610400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:90605800-90610400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr5:90605800-90611200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:90606000-90611200	Enhancers	Fetal Thymus	thymus
7	chr5:90606400-90609400	Enhancers	Lung	lung
8	chr5:90606400-90610400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:90606400-90610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:90606600-90610400	Enhancers	Primary T cells from cord blood	blood
11	chr5:90606600-90610600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:90606600-90612200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:90606800-90609400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr5:90606800-90609800	Enhancers	NHLF	lung
15	chr5:90606800-90610200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr5:90606800-90610600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:90606800-90611400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:90607000-90609600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr5:90607000-90609800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:90607000-90610200	Enhancers	Thymus	Thymus
21	chr5:90607000-90610400	Enhancers	Fetal Muscle Leg	muscle
22	chr5:90607000-90610600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr5:90607200-90609200	Enhancers	Brain Substantia Nigra	brain
24	chr5:90607200-90609200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr5:90607200-90609800	Enhancers	Brain Anterior Caudate	brain
26	chr5:90607200-90610200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr5:90607200-90610400	Enhancers	Brain Angular Gyrus	brain
28	chr5:90607200-90610600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr5:90607400-90610600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr5:90607400-90610600	Enhancers	Placenta Amnion	Placenta Amnion
31	chr5:90607600-90609600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr5:90607600-90609800	Enhancers	HepG2	liver
33	chr5:90607600-90609800	Enhancers	HMEC	breast
34	chr5:90607600-90609800	Enhancers	HUVEC	blood vessel
35	chr5:90607600-90610600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:90607600-90611400	Enhancers	K562	blood
37	chr5:90607800-90609200	Weak transcription	Spleen	Spleen
38	chr5:90607800-90610600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr5:90607800-90610600	Enhancers	Rectal Smooth Muscle	rectum
40	chr5:90607800-90610600	Flanking Active TSS	Hela-S3	cervix
41	chr5:90607800-90611000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:90608000-90609400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr5:90608000-90609800	Weak transcription	Stomach Mucosa	stomach
44	chr5:90608000-90610600	Enhancers	Fetal Heart	heart
45	chr5:90608000-90610800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:90608200-90609200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:90608200-90609200	Active TSS	Primary B cells from cord blood	blood
48	chr5:90608200-90609200	Weak transcription	Right Atrium	heart
49	chr5:90608200-90609400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:90608200-90609600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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