Variant report

Variant	rs3824454
Chromosome Location	chr9:100953144-100953145
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100939196..100942358-chr9:100952088..100954820,4	MCF-7	breast:
2	chr9:100952914..100958060-chr9:101016344..101019894,9	MCF-7	breast:
3	chr9:100896828..100898898-chr9:100952325..100954210,2	K562	blood:
4	chr9:100951866..100957184-chr9:101014234..101020511,10	K562	blood:
5	chr9:100932527..100936703-chr9:100952110..100957364,6	MCF-7	breast:
6	chr9:100879224..100881546-chr9:100952036..100953607,2	MCF-7	breast:
7	chr9:100952199..100954695-chr9:100957518..100959122,2	K562	blood:
8	chr9:100951009..100953373-chr9:100973381..100975463,2	K562	blood:
9	chr9:100746284..100748016-chr9:100953069..100955569,2	MCF-7	breast:
10	chr9:100934419..100936711-chr9:100950978..100955014,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction
ENSG00000106789	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10818590	1.00[CHB][hapmap];0.84[JPT][hapmap];0.99[ASN][1000 genomes]
rs10818610	0.80[GIH][hapmap]
rs10985365	1.00[ASW][hapmap];1.00[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];0.98[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]
rs10985369	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985370	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10985384	0.95[ASN][1000 genomes]
rs10985385	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12344700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555858	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575630	0.99[ASN][1000 genomes]
rs7029397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029784	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034562	0.99[ASN][1000 genomes]
rs7870439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
6	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3824454	CORO2A	cis	lymphoblastoid	seeQTL
rs3824454	CDC14B	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100931800-100954400	Weak transcription	Right Atrium	heart
2	chr9:100934400-100954000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:100935400-100953200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:100936000-100953200	Weak transcription	Gastric	stomach
5	chr9:100937800-100953200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:100941800-100954000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:100942800-100953400	Weak transcription	Primary T cells from cord blood	blood
8	chr9:100945000-100953600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:100948200-100953200	Weak transcription	Primary B cells from cord blood	blood
10	chr9:100948200-100953400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:100948200-100953400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:100948400-100953200	Weak transcription	Esophagus	oesophagus
13	chr9:100948400-100953600	Weak transcription	Spleen	Spleen
14	chr9:100948400-100954000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:100948600-100953600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:100948600-100953600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:100949200-100954200	Weak transcription	Small Intestine	intestine
18	chr9:100949600-100954000	Enhancers	Fetal Thymus	thymus
19	chr9:100950000-100953600	Enhancers	K562	blood
20	chr9:100950200-100953200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:100950600-100953800	Weak transcription	HMEC	breast
22	chr9:100951000-100953200	Weak transcription	Colonic Mucosa	Colon
23	chr9:100951200-100953600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:100951200-100953600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr9:100951400-100953200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr9:100951400-100953200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr9:100951400-100954000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr9:100951600-100953600	Weak transcription	Dnd41	blood
29	chr9:100951800-100953200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:100951800-100953200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:100952000-100953400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:100952000-100954000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:100952400-100953200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:100952400-100953600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr9:100952400-100953600	Enhancers	Stomach Mucosa	stomach
36	chr9:100952400-100953800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
37	chr9:100952400-100954000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr9:100952400-100954200	Enhancers	Liver	Liver
39	chr9:100952600-100953800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr9:100952600-100953800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:100952600-100953800	Enhancers	Thymus	Thymus
42	chr9:100952600-100954000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr9:100952600-100954000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr9:100952600-100954400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr9:100952800-100953200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:100952800-100953200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr9:100952800-100953400	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr9:100952800-100953800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:100952800-100953800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:100952800-100953800	Enhancers	Placenta Amnion	Placenta Amnion

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