Variant report

Variant	rs10838587
Chromosome Location	chr11:46272585-46272586
allele	C/T
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	chr11:46268842..46272928-chr11:46292404..46297152,6	K562	blood:
2	chr11:46262681..46266586-chr11:46271092..46274649,4	MCF-7	breast:
3	chr11:46267736..46276529-chr11:46293070..46299071,10	MCF-7	breast:
4	chr11:46271728..46274658-chr11:46298352..46303113,8	K562	blood:
5	chr11:46271383..46273893-chr11:46301365..46303113,2	K562	blood:
6	chr11:46270887..46273144-chr11:46314819..46316692,2	MCF-7	breast:
7	chr11:46271276..46274167-chr11:46310420..46312891,2	K562	blood:
8	chr11:46258381..46272821-chr11:46315090..46322037,29	K562	blood:
9	chr11:46270148..46272970-chr11:46357084..46359054,2	K562	blood:
10	chr11:46270210..46274167-chr11:46310420..46313245,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255007	Chromatin interaction
ENSG00000157613	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10838586	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10838588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10838589	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10838590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038812	0.85[JPT][hapmap]
rs11038834	0.89[GIH][hapmap];0.82[JPT][hapmap]
rs12225704	0.94[ASN][1000 genomes]
rs13377401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128258	0.84[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051344	chr11:46188818-46306447	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv541028	chr11:46188818-46306447	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv308	chr11:46242287-46287542	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10838587	MADD	cis	parietal	SCAN
rs10838587	PRDM11	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46265400-46273200	Weak transcription	Fetal Thymus	thymus
2	chr11:46265600-46273000	Weak transcription	Pancreas	Pancrea
3	chr11:46265600-46281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:46266400-46273600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:46268200-46272800	Enhancers	NHDF-Ad	bronchial
6	chr11:46268200-46272800	Enhancers	NHLF	lung
7	chr11:46268200-46273800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:46268200-46275800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:46268400-46274200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:46268600-46274200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:46269000-46276400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr11:46269200-46272600	Enhancers	HSMMtube	muscle
13	chr11:46269200-46274800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:46269400-46276400	Enhancers	Fetal Intestine Small	intestine
15	chr11:46269600-46272800	Weak transcription	Gastric	stomach
16	chr11:46270000-46276200	Enhancers	Fetal Intestine Large	intestine
17	chr11:46270800-46272600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr11:46271000-46273200	Weak transcription	Small Intestine	intestine
19	chr11:46271200-46273200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:46271200-46275200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr11:46271200-46276200	Enhancers	Duodenum Mucosa	Duodenum
22	chr11:46271200-46286600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:46271400-46272600	Weak transcription	Placenta	Placenta
24	chr11:46271400-46273000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:46271400-46273400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:46271400-46273400	Weak transcription	Left Ventricle	heart
27	chr11:46271400-46273800	Enhancers	Stomach Mucosa	stomach
28	chr11:46271400-46274800	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:46271400-46275000	Weak transcription	Fetal Heart	heart
30	chr11:46271400-46275400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:46271400-46275800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:46271800-46272800	Enhancers	Osteobl	bone
33	chr11:46272000-46273600	Bivalent Enhancer	HepG2	liver
34	chr11:46272200-46273800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr11:46272200-46276200	Enhancers	K562	blood
36	chr11:46272400-46273600	Weak transcription	Hela-S3	cervix
37	chr11:46272400-46273800	Weak transcription	A549	lung
38	chr11:46272400-46276000	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links