Variant report

Variant	rs10898223
Chromosome Location	chr11:71219264-71219265
allele	A/G
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	SETDB1	chr11:71219135-71219514	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71214959..71216939-chr11:71218643..71221307,2	K562	blood:
2	chr11:71214307..71215980-chr11:71218058..71219909,2	K562	blood:

Variant related genes	Relation type
ENSG00000254924	TF binding region
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10898186	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898191	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898201	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10898203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898211	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898228	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898241	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11233977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11234030	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11234042	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790349	0.80[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1792239	0.85[YRI][hapmap]
rs1792240	0.85[YRI][hapmap]
rs28762388	0.83[EUR][1000 genomes]
rs3829251	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7103591	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7114252	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7120029	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7130829	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7949129	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
3	nsv468632	chr11:71200320-71289089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv555402	chr11:71200320-71289089	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10898223	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10898223	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs10898223	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs10898223	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs10898223	NADSYN1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71210400-71220200	Weak transcription	NHEK	skin
2	chr11:71211800-71220600	Weak transcription	NH-A	brain
3	chr11:71211800-71232400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:71212000-71220600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:71213000-71219600	Weak transcription	Primary B cells from cord blood	blood
6	chr11:71213000-71220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:71213200-71220600	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:71213200-71232200	Weak transcription	Brain Angular Gyrus	brain
9	chr11:71214600-71220000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:71214800-71219400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:71215000-71222400	Weak transcription	HSMM	muscle
12	chr11:71215400-71219600	Weak transcription	Left Ventricle	heart
13	chr11:71215600-71219400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:71215600-71220600	Weak transcription	Colonic Mucosa	Colon
15	chr11:71215600-71236600	Weak transcription	Brain Anterior Caudate	brain
16	chr11:71215800-71219400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:71216000-71220000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:71216400-71235400	Weak transcription	Brain Substantia Nigra	brain
19	chr11:71216600-71219800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:71217000-71222000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:71217400-71219400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:71217400-71219800	Weak transcription	Gastric	stomach
23	chr11:71217400-71220400	Weak transcription	Adipose Nuclei	Adipose
24	chr11:71217400-71220400	Weak transcription	Fetal Intestine Large	intestine
25	chr11:71217600-71219600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:71217800-71219400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:71217800-71220000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:71217800-71221000	Weak transcription	Liver	Liver
29	chr11:71217800-71221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:71218000-71219600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:71218000-71220400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:71218000-71220600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:71218000-71220600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:71218000-71220600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr11:71218400-71219400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:71218400-71219800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:71218400-71219800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:71218400-71219800	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:71218400-71221000	Weak transcription	Fetal Intestine Small	intestine
40	chr11:71218400-71221200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:71218600-71219800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links