Variant report

Variant	rs62286042
Chromosome Location	chr4:8409506-8409507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8393388..8395511-chr4:8408173..8409725,2	MCF-7	breast:
2	chr4:8184952..8186912-chr4:8408862..8412072,3	MCF-7	breast:
3	chr4:8243346..8245051-chr4:8408250..8411036,2	K562	blood:

Variant related genes	Relation type
ENSG00000202054	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1060617	1.00[EUR][1000 genomes]
rs1106591	0.91[AMR][1000 genomes]
rs13434465	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16842352	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17194220	1.00[EUR][1000 genomes]
rs17201848	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17202499	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17203215	0.82[AMR][1000 genomes]
rs17203243	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17806817	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17806883	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17807929	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17807994	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28507650	1.00[EUR][1000 genomes]
rs28664136	1.00[EUR][1000 genomes]
rs61739067	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62286002	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286003	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286005	1.00[EUR][1000 genomes]
rs62286035	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286036	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286037	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286038	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286040	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286041	1.00[EUR][1000 genomes]
rs62286043	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286044	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62286047	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286049	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286050	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286052	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286053	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286054	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286055	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286056	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286058	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62286059	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62287360	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62287361	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62287362	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62287382	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287383	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287384	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287385	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287387	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287390	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287392	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62287393	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287394	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287395	0.91[AMR][1000 genomes]
rs62287396	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287397	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287399	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287401	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287402	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287405	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287406	0.80[EUR][1000 genomes]
rs62287433	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287434	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62287435	0.82[AMR][1000 genomes]
rs62287436	0.80[EUR][1000 genomes]
rs62287439	0.82[AMR][1000 genomes]
rs62287440	0.82[AMR][1000 genomes]
rs62287441	0.82[AMR][1000 genomes]
rs7686109	1.00[EUR][1000 genomes]
rs940132	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv593639	chr4:8394376-8424108	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
4	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:8389800-8411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:8395800-8411800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:8396600-8419400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:8396800-8412400	Weak transcription	Fetal Brain Male	brain
10	chr4:8396800-8415600	Weak transcription	NH-A	brain
11	chr4:8397600-8420400	Weak transcription	NHDF-Ad	bronchial
12	chr4:8399200-8412000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:8399400-8411800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:8399400-8412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:8399600-8412000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:8399600-8429400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:8403200-8419400	Strong transcription	Fetal Intestine Small	intestine
18	chr4:8403400-8411400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:8403400-8414400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:8403600-8412200	Strong transcription	Brain Germinal Matrix	brain
21	chr4:8404400-8410000	Weak transcription	NHLF	lung
22	chr4:8404600-8411800	Weak transcription	NHEK	skin
23	chr4:8404600-8429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:8404800-8411400	Weak transcription	Right Atrium	heart
25	chr4:8404800-8420600	Weak transcription	Psoas Muscle	Psoas
26	chr4:8405000-8411200	Weak transcription	HMEC	breast
27	chr4:8405000-8412200	Weak transcription	HUVEC	blood vessel
28	chr4:8405000-8415600	Weak transcription	Fetal Kidney	kidney
29	chr4:8405200-8410600	Strong transcription	HSMMtube	muscle
30	chr4:8405200-8411800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:8405200-8412200	Strong transcription	Spleen	Spleen
32	chr4:8405400-8410400	Strong transcription	Fetal Muscle Leg	muscle
33	chr4:8405400-8410400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr4:8405400-8411000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr4:8405400-8411000	Strong transcription	Placenta	Placenta
36	chr4:8405400-8411400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:8405400-8411800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:8405400-8412000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr4:8405400-8414400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:8405400-8418400	Strong transcription	Brain Hippocampus Middle	brain
41	chr4:8405600-8410400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:8405600-8411600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:8405600-8412600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:8405600-8418600	Strong transcription	Liver	Liver
45	chr4:8405600-8418800	Strong transcription	Aorta	Aorta
46	chr4:8405800-8411200	Strong transcription	Esophagus	oesophagus
47	chr4:8405800-8411200	Strong transcription	Ovary	ovary
48	chr4:8406000-8411400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:8406200-8409800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr4:8406200-8410200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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