Variant report

Variant	rs2081474
Chromosome Location	chr4:143489566-143489567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143488759..143491260-chr4:143536558..143538874,2	MCF-7	breast:
2	chr4:143488482..143490655-chr4:143513753..143516838,3	MCF-7	breast:
3	chr4:143484926..143487253-chr4:143488891..143490780,2	MCF-7	breast:
4	chr4:143479700..143482355-chr4:143488680..143491605,2	MCF-7	breast:
5	chr4:143391847..143398603-chr4:143487301..143496810,15	MCF-7	breast:
6	chr4:143389165..143391591-chr4:143488298..143490460,2	MCF-7	breast:
7	chr4:143391421..143397876-chr4:143484529..143495051,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249806	Chromatin interaction
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1017527	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1019643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857396	0.81[EUR][1000 genomes]
rs1116689	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12645567	0.89[EUR][1000 genomes]
rs13102826	0.80[AMR][1000 genomes]
rs13120964	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13147451	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs13149611	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs1373038	0.83[AMR][1000 genomes]
rs1425522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1443184	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1443188	0.83[CEU][hapmap]
rs1443189	0.83[AMR][1000 genomes]
rs1443190	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs17016514	0.91[CHB][hapmap]
rs17729514	0.91[CEU][hapmap]
rs1814061	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1838085	0.80[AMR][1000 genomes]
rs2120159	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs2120160	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2197215	0.83[AMR][1000 genomes]
rs4690722	0.81[AMR][1000 genomes]
rs6537122	0.83[AMR][1000 genomes]
rs6845652	0.89[EUR][1000 genomes]
rs7376422	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7670457	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7671783	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs7675305	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs7682731	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs7688435	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs978361	0.84[CEU][hapmap]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143486800-143489600	Active TSS	Primary T cells fromperipheralblood	blood
2	chr4:143486800-143489800	Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr4:143486800-143489800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:143487000-143489600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr4:143487000-143489600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:143487000-143489600	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr4:143487000-143489600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr4:143487000-143489800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:143487000-143489800	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr4:143487400-143491800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:143487600-143490000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:143487800-143489600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:143488200-143489600	Active TSS	Duodenum Mucosa	Duodenum
14	chr4:143488200-143489800	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr4:143488400-143489600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:143488400-143489600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:143488400-143489600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr4:143488400-143489600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:143488400-143489600	Active TSS	Fetal Intestine Small	intestine
20	chr4:143488400-143489600	Active TSS	Stomach Smooth Muscle	stomach
21	chr4:143488400-143489800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:143488400-143489800	Active TSS	A549	lung
23	chr4:143488400-143490800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr4:143488400-143493400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:143488600-143489600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:143488600-143490200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:143488600-143493400	Weak transcription	Left Ventricle	heart
28	chr4:143488800-143489600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:143488800-143489600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:143488800-143490200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr4:143489000-143489600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr4:143489000-143489600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:143489000-143489600	Enhancers	NH-A	brain
34	chr4:143489000-143489800	Active TSS	NHDF-Ad	bronchial
35	chr4:143489000-143490000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:143489000-143490000	Enhancers	Fetal Heart	heart
37	chr4:143489200-143489600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:143489200-143489600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr4:143489200-143489600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr4:143489200-143489600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr4:143489200-143489600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr4:143489200-143490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:143489200-143493200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:143489400-143489600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:143489400-143489600	Flanking Active TSS	Aorta	Aorta
46	chr4:143489400-143489600	Weak transcription	Fetal Intestine Large	intestine
47	chr4:143489400-143489600	Enhancers	HMEC	breast
48	chr4:143489400-143489600	Flanking Active TSS	NHLF	lung
49	chr4:143489400-143489600	Flanking Active TSS	Osteobl	bone
50	chr4:143489400-143490400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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