Variant report

Variant	rs10840269
Chromosome Location	chr11:9628802-9628803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9628381..9630279-chr11:9630483..9632846,2	K562	blood:
2	chr11:9628308..9628896-chr11:9770047..9770638,2	MCF-7	breast:
3	chr11:9479980..9482925-chr11:9627285..9628824,2	MCF-7	breast:
4	chr11:9628715..9629243-chr11:9769841..9770445,2	MCF-7	breast:
5	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
6	chr11:9625163..9627064-chr11:9628384..9630291,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000238387	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10770043	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs10770047	0.94[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840270	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs10840271	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12273601	0.98[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12419525	0.91[ASN][1000 genomes]
rs12420438	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2289074	0.82[TSI][hapmap]
rs3763869	0.81[CHB][hapmap]
rs57701122	0.82[AMR][1000 genomes]
rs7124238	0.82[AMR][1000 genomes];0.89[EUR][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	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv971986	chr11:9625730-9628863	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10840269	CYB5R2	cis	parietal	SCAN
rs10840269	SWAP70	cis	lymphoblastoid	seeQTL
rs10840269	SWAP70	cis	multi-tissue	Pritchard
rs10840269	PTH	cis	cerebellum	SCAN
rs10840269	SNORA23	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9597200-9635000	Weak transcription	Pancreas	Pancrea
2	chr11:9610600-9635000	Weak transcription	Aorta	Aorta
3	chr11:9623400-9631600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:9623400-9634600	Weak transcription	Thymus	Thymus
5	chr11:9623600-9630400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:9623600-9631400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:9623600-9631600	Weak transcription	Placenta	Placenta
8	chr11:9623600-9633600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:9623600-9634200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:9623600-9634600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:9623600-9634800	Weak transcription	Esophagus	oesophagus
12	chr11:9623600-9635000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:9624200-9634800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:9624400-9634200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:9624400-9634200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:9624400-9635000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:9625800-9630000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr11:9626400-9629200	Enhancers	K562	blood
19	chr11:9626600-9630400	Weak transcription	GM12878-XiMat	blood
20	chr11:9626600-9632400	Weak transcription	Dnd41	blood
21	chr11:9628200-9629200	Enhancers	Fetal Intestine Small	intestine
22	chr11:9628400-9629400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr11:9628400-9629400	Flanking Active TSS	HepG2	liver
24	chr11:9628400-9629600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr11:9628400-9629800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr11:9628400-9630200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr11:9628400-9630600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr11:9628600-9629000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:9628600-9629200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr11:9628800-9629000	Flanking Active TSS	A549	lung
31	chr11:9628800-9629400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr11:9628800-9629400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr11:9628800-9629600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr11:9628800-9629600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr11:9628800-9634000	Weak transcription	Fetal Intestine Large	intestine
36	chr11:9628800-9634400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:9628800-9634800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links