Variant report

Variant	rs859003
Chromosome Location	chr1:158148054-158148055
allele	C/T
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	CTCF	chr1:158147922-158148090	K562	blood:	n/a	n/a
2	TBL1XR1	chr1:158147915-158148104	K562	blood:	n/a	n/a
3	POLR2A	chr1:158146530-158148399	K562	blood:	n/a	n/a
4	CUX1	chr1:158147867-158148067	K562	blood:	n/a	n/a
5	MAZ	chr1:158147433-158148058	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
CD1D	TF binding region
ELL2P1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10489821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040592	0.91[CEU][hapmap]
rs12723141	0.95[JPT][hapmap]
rs1570699	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1633141	0.92[CEU][hapmap]
rs1633149	0.92[CEU][hapmap]
rs16839951	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1748383	0.92[CEU][hapmap]
rs1748387	0.92[CEU][hapmap]
rs1980757	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269715	0.80[JPT][hapmap]
rs2518477	0.92[CEU][hapmap]
rs3021476	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3021478	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087213	0.82[EUR][1000 genomes]
rs3118165	0.92[CEU][hapmap]
rs368130	0.92[CEU][hapmap]
rs374513	0.92[CEU][hapmap]
rs377795	0.92[CEU][hapmap]
rs383688	0.92[CEU][hapmap]
rs384414	0.92[CEU][hapmap]
rs389495	0.91[CEU][hapmap]
rs393304	0.84[CEU][hapmap]
rs401904	0.92[CEU][hapmap]
rs402699	0.92[CEU][hapmap]
rs407309	0.92[CEU][hapmap]
rs413557	0.92[CEU][hapmap]
rs434570	0.92[CEU][hapmap]
rs440862	0.92[CEU][hapmap]
rs448005	0.92[CEU][hapmap]
rs448556	0.92[CEU][hapmap]
rs449838	0.92[CEU][hapmap]
rs594364	0.92[CEU][hapmap]
rs607948	0.92[CEU][hapmap]
rs623215	0.92[CEU][hapmap]
rs6692064	0.92[EUR][1000 genomes]
rs6692133	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs691077	0.83[CEU][hapmap]
rs691175	0.92[CEU][hapmap]
rs691551	0.92[CEU][hapmap]
rs72711995	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72711999	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530662	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs7548147	1.00[JPT][hapmap]
rs7556487	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859001	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859002	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859009	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859010	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859011	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859013	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158143800-158149000	Weak transcription	Small Intestine	intestine
2	chr1:158147000-158148200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:158147000-158148200	Active TSS	HSMMtube	muscle
4	chr1:158147000-158148400	Active TSS	Psoas Muscle	Psoas
5	chr1:158147000-158150000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:158147000-158150400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:158147200-158148200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:158147200-158148200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr1:158147200-158148200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:158147200-158148200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:158147200-158148200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:158147200-158148200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:158147200-158148200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:158147200-158148200	Active TSS	Fetal Muscle Leg	muscle
15	chr1:158147200-158148200	Active TSS	Right Atrium	heart
16	chr1:158147200-158148200	Active TSS	Stomach Smooth Muscle	stomach
17	chr1:158147200-158148400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:158147200-158148400	Active TSS	Primary T cells from cord blood	blood
19	chr1:158147200-158148400	Active TSS	Adipose Nuclei	Adipose
20	chr1:158147200-158148400	Active TSS	Liver	Liver
21	chr1:158147400-158148200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr1:158147400-158148200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:158147400-158148200	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:158147400-158148200	Active TSS	Aorta	Aorta
25	chr1:158147400-158148200	Active TSS	Brain Angular Gyrus	brain
26	chr1:158147400-158148200	Active TSS	Fetal Thymus	thymus
27	chr1:158147400-158148200	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr1:158147400-158148400	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr1:158147400-158148400	Active TSS	Colonic Mucosa	Colon
30	chr1:158147400-158148400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:158147400-158148400	Bivalent/Poised TSS	A549	lung
32	chr1:158147400-158148600	Active TSS	Duodenum Mucosa	Duodenum
33	chr1:158147600-158148200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:158147600-158148200	Active TSS	Brain Substantia Nigra	brain
35	chr1:158147800-158148200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
36	chr1:158147800-158148200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:158147800-158148200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:158147800-158148200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr1:158147800-158148200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
40	chr1:158147800-158148200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
41	chr1:158147800-158148200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
42	chr1:158147800-158148200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr1:158147800-158148200	Flanking Active TSS	HMEC	breast
44	chr1:158147800-158148200	Bivalent/Poised TSS	NHDF-Ad	bronchial
45	chr1:158147800-158148400	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr1:158147800-158148400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:158147800-158148400	Bivalent/Poised TSS	Osteobl	bone
48	chr1:158147800-158149400	Weak transcription	Pancreas	Pancrea
49	chr1:158147800-158150400	Weak transcription	Left Ventricle	heart
50	chr1:158147800-158150600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links