Variant report

Variant	rs1873000
Chromosome Location	chr3:46029458-46029459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr3:46029317-46029695	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr3:46028886-46029623	HUVEC	blood vessel:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:45992659..45994641-chr3:46028942..46030792,2	K562	blood:
2	chr3:46021917..46024700-chr3:46027716..46030169,2	MCF-7	breast:
3	chr3:46024602..46026106-chr3:46028613..46030507,2	MCF-7	breast:
4	chr3:46028019..46029570-chr3:46035343..46037600,2	MCF-7	breast:
5	chr3:45986089..45986960-chr3:46029015..46029526,2	MCF-7	breast:
6	chr3:46019490..46020101-chr3:46029374..46029909,2	MCF-7	breast:
7	chr3:46026501..46029475-chr3:46032165..46035137,4	MCF-7	breast:

No data

Variant related genes	Relation type
FYCO1	TF binding region
ENSG00000163820	Chromatin interaction
ENSG00000172215	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11130082	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12053895	0.81[EUR][1000 genomes]
rs12485445	0.81[EUR][1000 genomes]
rs13064616	0.81[EUR][1000 genomes]
rs13084541	0.81[EUR][1000 genomes]
rs13086858	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1392298	0.80[EUR][1000 genomes]
rs1500003	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1545985	0.91[CEU][hapmap]
rs1846615	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1846616	0.84[EUR][1000 genomes]
rs1873001	0.91[CEU][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2129879	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2129881	0.81[EUR][1000 genomes]
rs2133660	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2171528	0.91[CEU][hapmap]
rs2171529	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2373089	0.81[EUR][1000 genomes]
rs2373090	0.81[EUR][1000 genomes]
rs35283688	0.81[EUR][1000 genomes]
rs4683159	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57542549	0.81[EUR][1000 genomes]
rs6774629	0.80[EUR][1000 genomes]
rs7612402	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7628447	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869609	0.80[EUR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1873000	FYCO1	cis	lung	GTEx
rs1873000	CCR3	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
5	chr3:46019400-46030000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
7	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:46023000-46029800	Strong transcription	Primary T cells from cord blood	blood
10	chr3:46025000-46031600	Weak transcription	Fetal Kidney	kidney
11	chr3:46025200-46031800	Enhancers	Right Atrium	heart
12	chr3:46025600-46032400	Enhancers	Stomach Mucosa	stomach
13	chr3:46025600-46033000	Enhancers	Right Ventricle	heart
14	chr3:46025800-46031200	Enhancers	HSMMtube	muscle
15	chr3:46026000-46031800	Enhancers	NHDF-Ad	bronchial
16	chr3:46026200-46029800	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr3:46026200-46031800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:46026200-46032000	Enhancers	Ovary	ovary
19	chr3:46026200-46032000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr3:46026200-46032000	Enhancers	NHLF	lung
21	chr3:46026400-46031400	Enhancers	HSMM	muscle
22	chr3:46026400-46031600	Enhancers	Fetal Intestine Large	intestine
23	chr3:46026400-46031800	Enhancers	Fetal Muscle Leg	muscle
24	chr3:46026400-46033800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:46026400-46034600	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr3:46026600-46029600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:46026600-46029800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:46026600-46030000	Enhancers	Colonic Mucosa	Colon
29	chr3:46026600-46031400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:46026600-46031400	Enhancers	Lung	lung
31	chr3:46026600-46031600	Enhancers	Pancreas	Pancrea
32	chr3:46026600-46031800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:46026600-46032200	Enhancers	Liver	Liver
34	chr3:46026600-46032200	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:46026600-46033000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:46026600-46033000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:46026600-46033000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:46026600-46036200	Enhancers	Left Ventricle	heart
39	chr3:46026800-46029800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:46026800-46032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:46026800-46033400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:46026800-46033600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:46026800-46033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:46026800-46035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:46027000-46029800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:46027000-46030000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:46027000-46030200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:46027000-46030200	Enhancers	Fetal Brain Female	brain
49	chr3:46027000-46030200	Enhancers	Placenta	Placenta
50	chr3:46027000-46031400	Enhancers	NH-A	brain

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