Variant report

Variant	rs56188890
Chromosome Location	chr11:70808985-70808986
allele	C/T
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	CTCF	chr11:70808891-70809334	GM19239	blood:	n/a	n/a
2	NR2C2	chr11:70808911-70809318	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:70808808-70809348	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr11:70808936-70809046	GM12878	blood:	n/a	chr11:70809015-70809025 chr11:70809031-70809041
5	MYC	chr11:70808953-70809078	MCF-7	breast:	n/a	chr11:70809015-70809025 chr11:70809031-70809041
6	SUZ12	chr11:70808886-70809394	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:70808871-70809127	MCF-7	breast:	n/a	n/a
8	POLR2A	chr11:70808950-70809271	Gliobla	brain:	n/a	n/a
9	MYC	chr11:70808894-70809118	MCF-7	breast:	n/a	chr11:70809015-70809025 chr11:70809031-70809041
10	POLR2A	chr11:70808808-70809137	MCF-7	breast:	n/a	n/a
11	MYC	chr11:70808956-70809311	MCF-7	breast:	n/a	chr11:70809015-70809025 chr11:70809031-70809041
12	POLR2A	chr11:70808850-70809318	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SHANK2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11823567	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12420697	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17431746	1.00[ASN][1000 genomes]
rs55753840	1.00[ASN][1000 genomes]
rs7123599	1.00[ASN][1000 genomes]
rs72957631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72957634	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72957637	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72957640	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72957676	1.00[ASN][1000 genomes]
rs72957677	1.00[ASN][1000 genomes]
rs72957679	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:70795400-70809000	Weak transcription	Fetal Kidney	kidney
2	chr11:70795800-70814200	Weak transcription	Stomach Mucosa	stomach
3	chr11:70796000-70820000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:70796600-70812800	Strong transcription	HepG2	liver
5	chr11:70799200-70811000	Strong transcription	Fetal Intestine Small	intestine
6	chr11:70799200-70823400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:70799800-70831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:70800600-70809000	Weak transcription	NHLF	lung
9	chr11:70800600-70850800	Weak transcription	Right Atrium	heart
10	chr11:70800800-70824400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:70801200-70824600	Strong transcription	Liver	Liver
12	chr11:70801400-70810400	Strong transcription	Fetal Stomach	stomach
13	chr11:70801600-70809400	Strong transcription	Fetal Intestine Large	intestine
14	chr11:70803600-70820200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:70805200-70809000	Weak transcription	A549	lung
16	chr11:70805400-70820000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:70805800-70819600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:70806000-70809000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:70806000-70820200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:70806200-70818000	Weak transcription	Placenta	Placenta
21	chr11:70806400-70809000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:70806400-70809000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:70806400-70820400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:70808000-70809600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:70808200-70813000	Weak transcription	HMEC	breast
26	chr11:70808600-70809000	Strong transcription	Gastric	stomach
27	chr11:70808800-70809000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:70808800-70809000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:70808800-70809000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
30	chr11:70808800-70809200	Bivalent Enhancer	Fetal Brain Male	brain
31	chr11:70808800-70809400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:70808800-70809400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:70808800-70809400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr11:70808800-70809400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:70808800-70809400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:70808800-70809400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr11:70808800-70809400	ZNF genes & repeats	Lung	lung
38	chr11:70808800-70809400	Strong transcription	Pancreas	Pancrea
39	chr11:70808800-70809400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr11:70808800-70809800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr11:70808800-70809800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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