Variant report

Variant	rs10888585
Chromosome Location	chr1:150504947-150504948
allele	G/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150457160..150457987-chr1:150504714..150505677,5	MCF-7	breast:
2	chr1:150458457..150460926-chr1:150503532..150505765,2	K562	blood:
3	chr1:150503877..150505542-chr1:150592615..150595135,2	K562	blood:
4	chr1:150500611..150502292-chr1:150503281..150505329,2	MCF-7	breast:
5	chr1:150503285..150505539-chr1:150516605..150518473,3	K562	blood:
6	chr1:150504741..150505587-chr1:150531856..150532693,3	MCF-7	breast:
7	chr1:150435913..150437484-chr1:150504730..150505672,10	MCF-7	breast:
8	chr1:150459747..150461313-chr1:150503560..150505581,2	MCF-7	breast:
9	chr1:150501374..150507870-chr1:150516377..150523612,9	K562	blood:
10	chr1:150457130..150458050-chr1:150504820..150505453,2	MCF-7	breast:
11	chr1:150501937..150505214-chr1:150520640..150523168,3	K562	blood:
12	chr1:150504726..150505589-chr1:150532122..150532627,2	K562	blood:
13	chr1:150457403..150459497-chr1:150504358..150506324,2	MCF-7	breast:
14	chr1:150502838..150505562-chr1:150511108..150512922,2	K562	blood:
15	chr1:150503131..150505095-chr1:150506786..150509617,2	MCF-7	breast:
16	chr1:150458185..150460398-chr1:150503191..150505589,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143382	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000143374	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11205363	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12027008	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs16837432	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs60162170	0.85[ASN][1000 genomes]
rs6694485	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	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
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10888585	TARS2	cis	cerebellum	SCAN
rs10888585	MCL1	cis	lymphoblastoid	seeQTL
rs10888585	C1orf54	cis	parietal	SCAN
rs10888585	ARNT	cis	cerebellum	SCAN
rs10888585	C1orf54	cis	cerebellum	SCAN
rs10888585	ECM1	cis	cerebellum	SCAN
rs10888585	CTSS	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150489000-150505400	Weak transcription	Right Ventricle	heart
2	chr1:150500600-150505000	Weak transcription	Fetal Stomach	stomach
3	chr1:150500800-150505000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:150502000-150505000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:150502000-150505000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:150502000-150505200	Weak transcription	Esophagus	oesophagus
7	chr1:150502000-150505200	Weak transcription	Hela-S3	cervix
8	chr1:150502000-150505400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:150502000-150510800	Weak transcription	Aorta	Aorta
10	chr1:150502200-150505400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:150502200-150506400	Weak transcription	Right Atrium	heart
12	chr1:150502600-150505000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:150502600-150505000	Weak transcription	NHDF-Ad	bronchial
14	chr1:150502600-150505200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:150503200-150506000	Enhancers	K562	blood
16	chr1:150504000-150507000	Enhancers	Fetal Intestine Large	intestine
17	chr1:150504200-150505000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:150504200-150505400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:150504200-150505600	Flanking Active TSS	HepG2	liver
20	chr1:150504200-150505800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:150504200-150505800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:150504200-150505800	Enhancers	Pancreas	Pancrea
23	chr1:150504200-150505800	Enhancers	NH-A	brain
24	chr1:150504200-150506000	Enhancers	Placenta	Placenta
25	chr1:150504200-150506600	Enhancers	Stomach Mucosa	stomach
26	chr1:150504200-150506800	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:150504200-150507000	Enhancers	Fetal Intestine Small	intestine
28	chr1:150504200-150507000	Enhancers	HMEC	breast
29	chr1:150504200-150507600	Enhancers	Colonic Mucosa	Colon
30	chr1:150504200-150511200	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:150504200-150511600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:150504400-150505400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:150504400-150505400	Weak transcription	Gastric	stomach
34	chr1:150504600-150505000	Enhancers	Osteobl	bone
35	chr1:150504600-150505200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:150504600-150505200	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr1:150504600-150505600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:150504600-150505800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:150504600-150506000	Enhancers	Adipose Nuclei	Adipose
40	chr1:150504600-150507000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:150504600-150511600	Enhancers	Fetal Muscle Leg	muscle
42	chr1:150504800-150505000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:150504800-150505000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:150504800-150505200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:150504800-150505200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:150504800-150505200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:150504800-150505200	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr1:150504800-150505200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr1:150504800-150505200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr1:150504800-150505200	Flanking Active TSS	HSMM	muscle

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