Variant report

Variant	rs11550558
Chromosome Location	chr12:56386076-56386077
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56384934..56392097-chr12:56507991..56512680,9	MCF-7	breast:
2	chr12:56365739..56372949-chr12:56384756..56392202,12	MCF-7	breast:
3	chr12:56324272..56327111-chr12:56385454..56388039,2	MCF-7	breast:
4	chr12:56383457..56387356-chr12:56388448..56393059,5	MCF-7	breast:
5	chr12:56386022..56392601-chr12:56434180..56439537,11	MCF-7	breast:
6	chr12:56384784..56387430-chr12:56389499..56392081,3	MCF-7	breast:
7	chr12:56382696..56386085-chr12:56510688..56513603,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUOX-1	chr12:56385991-56388469	NONHSAT028732

No data

Variant related genes	Relation type
ENSG00000139531	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045435	0.88[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783777	1.00[ASN][1000 genomes]
rs10783778	1.00[ASN][1000 genomes]
rs10876867	1.00[ASN][1000 genomes]
rs1091527	1.00[ASN][1000 genomes]
rs11171713	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11171714	0.87[EUR][1000 genomes]
rs11171715	0.90[EUR][1000 genomes]
rs11835310	1.00[ASN][1000 genomes]
rs11837075	0.87[ASN][1000 genomes]
rs12815387	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs12817765	0.94[EUR][1000 genomes]
rs12831884	0.88[CEU][hapmap]
rs1614219	1.00[ASN][1000 genomes]
rs1626158	1.00[ASN][1000 genomes]
rs1689511	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs1689517	1.00[ASN][1000 genomes]
rs1689518	1.00[ASN][1000 genomes]
rs1701706	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118206	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17118208	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2069391	0.90[GIH][hapmap]
rs2271193	1.00[ASN][1000 genomes]
rs2271195	1.00[ASN][1000 genomes]
rs2277340	1.00[ASN][1000 genomes]
rs2456972	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs2640566	1.00[ASN][1000 genomes]
rs2658479	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs2661728	1.00[ASN][1000 genomes]
rs2661729	1.00[ASN][1000 genomes]
rs2934152	1.00[ASN][1000 genomes]
rs3213122	0.90[GIH][hapmap]
rs34071823	0.94[EUR][1000 genomes]
rs34273234	0.92[EUR][1000 genomes]
rs34962186	0.94[EUR][1000 genomes]
rs4759022	0.85[CEU][hapmap]
rs67594137	0.92[EUR][1000 genomes]
rs705700	0.81[LWK][hapmap]
rs71447768	0.94[EUR][1000 genomes]
rs71459326	0.94[EUR][1000 genomes]
rs71459327	0.94[EUR][1000 genomes]
rs7300292	1.00[ASN][1000 genomes]
rs7304690	1.00[ASN][1000 genomes]
rs73338377	1.00[ASN][1000 genomes]
rs73338385	1.00[ASN][1000 genomes]
rs73338396	0.87[ASN][1000 genomes]
rs772922	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs772923	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs773114	0.83[YRI][hapmap]
rs773115	1.00[ASN][1000 genomes]
rs7970035	1.00[ASN][1000 genomes]
rs9738143	1.00[ASN][1000 genomes]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11550558	RPS26	cis	lymphoblastoid	seeQTL
rs11550558	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
5	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:56370400-56388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:56370600-56388200	Strong transcription	Dnd41	blood
8	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:56371600-56388800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56372400-56390000	Strong transcription	Placenta	Placenta
12	chr12:56372800-56386200	Strong transcription	Fetal Intestine Large	intestine
13	chr12:56372800-56389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:56372800-56389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:56372800-56389600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:56373200-56386600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:56373400-56389400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:56373400-56389600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:56373600-56388600	Strong transcription	Liver	Liver
20	chr12:56374000-56388600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:56374000-56389600	Strong transcription	Fetal Stomach	stomach
22	chr12:56374200-56388800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:56375800-56390600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:56376000-56389600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:56376600-56388200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:56376600-56388800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:56376600-56389600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:56377000-56389400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:56377200-56388600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:56377200-56389200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:56377400-56388200	Strong transcription	Brain Anterior Caudate	brain
32	chr12:56377400-56388400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:56377400-56388600	Strong transcription	Thymus	Thymus
34	chr12:56377400-56389400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:56377600-56389000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:56377600-56389200	Strong transcription	Adipose Nuclei	Adipose
37	chr12:56377600-56389600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:56377800-56388600	Strong transcription	Brain Germinal Matrix	brain
39	chr12:56377800-56389200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:56377800-56389600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:56378000-56389600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:56378200-56388800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:56378200-56389600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:56378400-56388800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:56378400-56389400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:56378400-56389400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:56378400-56389600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:56378600-56389000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr12:56378600-56389400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr12:56378800-56388200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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