Variant report

Variant	rs1049403
Chromosome Location	chr11:9610805-9610806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9548599..9552302-chr11:9610096..9614093,4	K562	blood:
2	chr11:9608984..9611660-chr11:9632383..9635489,3	K562	blood:
3	chr11:9596567..9599546-chr11:9610760..9612310,2	MCF-7	breast:
4	chr11:9589366..9592285-chr11:9609804..9612652,2	MCF-7	breast:
5	chr11:9609396..9611431-chr11:9633989..9636334,2	K562	blood:

Variant related genes	Relation type
ENSG00000166483	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10770041	0.94[ASN][1000 genomes]
rs10770042	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840263	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840265	0.95[ASN][1000 genomes]
rs10840266	0.96[ASN][1000 genomes]
rs11042426	0.81[EUR][1000 genomes]
rs11042429	0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs11042431	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12799030	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35981065	0.88[EUR][1000 genomes]
rs4910482	0.94[ASN][1000 genomes]
rs7107252	0.96[ASN][1000 genomes]
rs7110225	0.91[ASN][1000 genomes]
rs7131557	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7940672	0.86[AMR][1000 genomes];0.87[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	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1049403	OR2D3	cis	cerebellum	SCAN
rs1049403	DKK3	cis	cerebellum	SCAN
rs1049403	SWAP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9597000-9613400	Weak transcription	Gastric	stomach
2	chr11:9597000-9622000	Weak transcription	Spleen	Spleen
3	chr11:9597200-9635000	Weak transcription	Pancreas	Pancrea
4	chr11:9597600-9615200	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:9598400-9612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:9598800-9611600	Strong transcription	Primary hematopoietic stem cells	blood
7	chr11:9599200-9612200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:9599400-9612200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:9599400-9612400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:9599400-9612400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:9599400-9612400	Strong transcription	Fetal Thymus	thymus
12	chr11:9599600-9611200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:9599600-9622800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:9599800-9612400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:9599800-9617000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:9599800-9622400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:9600000-9611600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:9600000-9612000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:9600000-9612400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:9600200-9612000	Strong transcription	Osteobl	bone
21	chr11:9600200-9612600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:9600200-9612600	Strong transcription	HUVEC	blood vessel
23	chr11:9600200-9613400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:9600400-9612400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:9600400-9612600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:9600600-9612200	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:9600800-9611400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:9600800-9612200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:9601000-9611000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:9601000-9611400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:9601000-9611400	Strong transcription	Fetal Lung	lung
32	chr11:9601000-9612000	Strong transcription	Liver	Liver
33	chr11:9601000-9612200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:9601000-9612400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:9601000-9612400	Strong transcription	NH-A	brain
36	chr11:9601000-9612600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:9601200-9611000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:9601200-9611200	Strong transcription	A549	lung
39	chr11:9601200-9611400	Strong transcription	HepG2	liver
40	chr11:9601200-9612000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:9601400-9611000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:9601400-9611600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr11:9601400-9611600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr11:9601400-9612200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:9601400-9612400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:9601400-9612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:9601400-9612400	Strong transcription	Fetal Intestine Large	intestine
48	chr11:9601400-9612400	Strong transcription	Placenta	Placenta
49	chr11:9601400-9613200	Strong transcription	NHDF-Ad	bronchial
50	chr11:9601400-9622600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links