Variant report

Variant	rs7558950
Chromosome Location	chr2:54752346-54752347
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	PBX3	chr2:54751670-54752351	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr2:54752240-54752390	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54752145..54754517-chr2:54758567..54761057,2	MCF-7	breast:
2	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:
3	chr2:54747821..54752887-chr2:54784386..54788690,5	MCF-7	breast:

Variant related genes	Relation type
RPL23AP32	TF binding region
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10165490	0.85[EUR][1000 genomes]
rs10180713	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1047499	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11892788	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11898012	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12104998	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12105792	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467581	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12468469	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12617036	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713260	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13016942	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13399435	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1367295	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1541854	0.89[EUR][1000 genomes]
rs17344044	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17344072	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17521078	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1802889	0.85[EUR][1000 genomes]
rs1864493	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292356	0.84[EUR][1000 genomes]
rs2941586	0.84[EUR][1000 genomes]
rs2941587	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2941595	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2971877	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2971879	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2971883	0.81[AFR][1000 genomes]
rs2971887	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3796014	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4233952	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4233954	0.85[EUR][1000 genomes]
rs4444573	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4455199	0.89[EUR][1000 genomes]
rs4514917	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4519562	0.87[EUR][1000 genomes]
rs4592889	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671221	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671222	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671225	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671226	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4671945	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671946	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671947	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671949	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671950	0.85[EUR][1000 genomes]
rs4671951	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671954	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671955	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671956	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4990319	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545411	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545413	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545414	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545415	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545418	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545419	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545427	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545429	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545434	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6704769	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6706372	0.89[EUR][1000 genomes]
rs6724590	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6729826	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731661	0.89[EUR][1000 genomes]
rs6732949	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6734658	0.89[EUR][1000 genomes]
rs6735813	0.88[EUR][1000 genomes]
rs6742607	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6746016	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6746306	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6748816	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6761369	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6761398	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7563706	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589236	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7607451	0.88[EUR][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	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7558950	EML6	cis	Thyroid	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
3	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
4	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:54744400-54753400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:54744400-54753400	Weak transcription	Ovary	ovary
9	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
10	chr2:54744600-54753400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:54747200-54753200	Weak transcription	Fetal Brain Female	brain
14	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:54747400-54753600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:54747800-54752400	Enhancers	Brain Hippocampus Middle	brain
18	chr2:54747800-54753400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:54748200-54753600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
22	chr2:54749200-54752400	Enhancers	A549	lung
23	chr2:54749600-54752400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:54749800-54752400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:54749800-54752400	Enhancers	Brain Angular Gyrus	brain
26	chr2:54749800-54752600	Enhancers	HMEC	breast
27	chr2:54750000-54752400	Enhancers	Brain Substantia Nigra	brain
28	chr2:54750000-54752600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:54750000-54752600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:54750000-54752600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:54750200-54752400	Enhancers	Hela-S3	cervix
32	chr2:54750200-54752800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:54750200-54753200	Enhancers	Fetal Heart	heart
34	chr2:54750400-54752400	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:54750400-54752400	Enhancers	Osteobl	bone
36	chr2:54750400-54752600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:54750400-54753400	Enhancers	Brain Anterior Caudate	brain
38	chr2:54750400-54753600	Enhancers	Right Ventricle	heart
39	chr2:54750600-54752600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:54750600-54752600	Enhancers	Adipose Nuclei	Adipose
41	chr2:54750600-54752600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:54750600-54753600	Enhancers	Left Ventricle	heart
43	chr2:54750600-54757000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:54750800-54752400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:54750800-54752400	Enhancers	HSMMtube	muscle
46	chr2:54750800-54753200	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:54750800-54753200	Enhancers	Placenta Amnion	Placenta Amnion
48	chr2:54750800-54753400	Weak transcription	Liver	Liver
49	chr2:54750800-54753600	Weak transcription	Brain Germinal Matrix	brain
50	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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