Variant report

Variant	rs61820165
Chromosome Location	chr1:150555987-150555988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
2	chr1:150554954..150558805-chr1:150562851..150567781,4	K562	blood:

Variant related genes	Relation type
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888384	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888385	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204668	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204669	0.93[ASN][1000 genomes]
rs11204675	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204677	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204678	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204679	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204680	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204684	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585169	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116492	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125672	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126271	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12139563	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12406712	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746899	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971378	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2048558	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738484	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738485	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970923	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971041	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55862611	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669122	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697620	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698495	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878471	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932054	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9803935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs61820165	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs61820165	GOLPH3L	cis	Nerve Tibial	GTEx
rs61820165	HORMAD1	cis	Esophagus Mucosa	GTEx
rs61820165	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs61820165	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs61820165	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs61820165	HORMAD1	cis	Nerve Tibial	GTEx
rs61820165	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs61820165	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs61820165	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs61820165	ARNT	cis	Thyroid	GTEx
rs61820165	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150556000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:150553000-150557000	Weak transcription	Fetal Stomach	stomach
3	chr1:150553000-150557200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:150553000-150559200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:150553000-150560600	Weak transcription	Right Atrium	heart
6	chr1:150553000-150562600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:150553000-150572800	Weak transcription	Thymus	Thymus
8	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:150553200-150558200	Weak transcription	Right Ventricle	heart
10	chr1:150553200-150564200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:150553200-150566000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:150553200-150568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:150553200-150569400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:150553200-150569400	Weak transcription	Fetal Thymus	thymus
15	chr1:150553200-150572600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:150553200-150572600	Weak transcription	Fetal Brain Female	brain
17	chr1:150553200-150572800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:150553200-150577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:150553200-150581800	Weak transcription	Dnd41	blood
21	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
23	chr1:150553400-150556400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:150553800-150568000	Weak transcription	HSMM	muscle
25	chr1:150553800-150572600	Weak transcription	Lung	lung
26	chr1:150553800-150576800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:150554000-150558400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:150554000-150560400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:150554000-150568400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:150554000-150568600	Weak transcription	Hela-S3	cervix
31	chr1:150554000-150572000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:150554200-150568400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:150554400-150572600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:150555400-150556000	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:150555400-150568400	Weak transcription	Osteobl	bone
37	chr1:150555400-150572600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
39	chr1:150555600-150556000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:150555600-150568400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:150555600-150568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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