Variant report

Variant	rs11121561
Chromosome Location	chr1:10461177-10461178
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10457490..10461716-chr1:10469511..10473951,6	K562	blood:
2	chr1:10404777..10406938-chr1:10460757..10462400,2	K562	blood:
3	chr1:10446399..10450088-chr1:10457513..10461303,7	MCF-7	breast:
4	chr1:10457403..10461622-chr1:10531171..10536559,7	K562	blood:
5	chr1:10446950..10451985-chr1:10457311..10462205,6	K562	blood:
6	chr1:10269508..10272201-chr1:10459062..10462119,3	K562	blood:
7	chr1:10446221..10450110-chr1:10457451..10462205,13	MCF-7	breast:
8	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265945	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000054523	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000271989	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1002076	0.93[ASN][1000 genomes]
rs10864450	0.82[EUR][1000 genomes]
rs10864453	0.90[EUR][1000 genomes]
rs11121541	0.88[EUR][1000 genomes]
rs11121551	0.92[ASN][1000 genomes]
rs11121555	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11121557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121560	0.94[ASN][1000 genomes]
rs11121563	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121566	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1138791	0.93[ASN][1000 genomes]
rs11576384	0.93[ASN][1000 genomes]
rs11579365	0.94[ASN][1000 genomes]
rs11585794	0.93[ASN][1000 genomes]
rs11586842	0.90[ASN][1000 genomes]
rs11587309	0.93[ASN][1000 genomes]
rs11587495	0.91[ASN][1000 genomes]
rs11587854	0.93[ASN][1000 genomes]
rs12118323	0.94[ASN][1000 genomes]
rs12128374	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12130563	0.81[ASN][1000 genomes]
rs12131441	0.81[ASN][1000 genomes]
rs12136404	0.81[EUR][1000 genomes]
rs12141201	0.93[ASN][1000 genomes]
rs12402723	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12409754	0.93[ASN][1000 genomes]
rs12738317	0.80[ASN][1000 genomes]
rs12746471	0.97[ASN][1000 genomes]
rs1467653	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1536262	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17396973	0.81[EUR][1000 genomes]
rs17402762	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2148152	0.81[ASN][1000 genomes]
rs2229687	0.94[ASN][1000 genomes]
rs2236678	0.94[ASN][1000 genomes]
rs34045426	0.92[ASN][1000 genomes]
rs34075302	0.88[ASN][1000 genomes]
rs34636442	0.80[ASN][1000 genomes]
rs35716098	0.94[ASN][1000 genomes]
rs35759975	0.94[ASN][1000 genomes]
rs35811280	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737155	0.97[ASN][1000 genomes]
rs3748575	0.82[EUR][1000 genomes]
rs3748579	0.80[ASN][1000 genomes]
rs3748581	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762286	0.94[ASN][1000 genomes]
rs3762287	0.92[ASN][1000 genomes]
rs3762288	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845930	0.81[EUR][1000 genomes]
rs4846216	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4846218	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4846219	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846221	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58014725	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61778399	0.81[ASN][1000 genomes]
rs61778401	0.81[ASN][1000 genomes]
rs61778402	0.81[ASN][1000 genomes]
rs61778404	0.88[ASN][1000 genomes]
rs6541090	0.89[EUR][1000 genomes]
rs6541094	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6674949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6682868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546368	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs912962	0.83[EUR][1000 genomes]
rs9651117	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11121561	PGD	cis	Muscle Skeletal	GTEx
rs11121561	PGD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10459200-10461200	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr1:10459400-10461200	Active TSS	Right Atrium	heart
3	chr1:10459600-10465000	Transcr. at gene 5' and 3'	A549	lung
4	chr1:10459800-10461200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:10459800-10461200	Flanking Active TSS	Liver	Liver
6	chr1:10460000-10461400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:10460000-10461600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
8	chr1:10460000-10461800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:10460000-10463800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
11	chr1:10460200-10461200	Enhancers	Colonic Mucosa	Colon
12	chr1:10460200-10461400	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr1:10460200-10461600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr1:10460200-10461800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:10460200-10475400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:10460400-10461200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:10460400-10461200	Enhancers	Fetal Brain Male	brain
18	chr1:10460400-10461400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:10460400-10462000	Active TSS	Esophagus	oesophagus
20	chr1:10460400-10462400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:10460400-10462800	Weak transcription	Primary T cells from cord blood	blood
22	chr1:10460400-10462800	Weak transcription	Aorta	Aorta
23	chr1:10460400-10462800	Weak transcription	Right Ventricle	heart
24	chr1:10460400-10462800	Weak transcription	Thymus	Thymus
25	chr1:10460400-10463000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:10460400-10463600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:10460400-10463800	Weak transcription	Gastric	stomach
28	chr1:10460400-10464200	Weak transcription	Pancreas	Pancrea
29	chr1:10460400-10464200	Weak transcription	Spleen	Spleen
30	chr1:10460400-10464800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:10460400-10472800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:10460400-10475200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:10460600-10461200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:10460600-10461400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
35	chr1:10460600-10461400	Active TSS	Adipose Nuclei	Adipose
36	chr1:10460600-10461400	Genic enhancers	Fetal Intestine Small	intestine
37	chr1:10460600-10461600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:10460600-10461600	Enhancers	Brain Hippocampus Middle	brain
39	chr1:10460600-10461600	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:10460600-10461600	Enhancers	HMEC	breast
41	chr1:10460600-10461600	Enhancers	NHDF-Ad	bronchial
42	chr1:10460600-10461800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:10460600-10461800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:10460600-10461800	Active TSS	NHLF	lung
45	chr1:10460600-10462000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:10460600-10462000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:10460600-10462000	Weak transcription	Fetal Intestine Large	intestine
48	chr1:10460600-10462200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:10460600-10462400	Weak transcription	Ovary	ovary
50	chr1:10460600-10462800	Weak transcription	Primary T cells fromperipheralblood	blood

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