Variant report

Variant	rs2793239
Chromosome Location	chr6:4994752-4994753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4991690..4994969-chr6:5000168..5002505,4	K562	blood:
2	chr6:4982368..4985908-chr6:4994564..4997355,3	K562	blood:
3	chr6:4994742..4997035-chr6:4997235..4999269,2	MCF-7	breast:
4	chr6:4994348..4996061-chr6:5002730..5005502,2	K562	blood:

Variant related genes	Relation type
ENSG00000124787	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1108041	0.81[ASN][1000 genomes]
rs11967778	1.00[JPT][hapmap]
rs11967814	1.00[JPT][hapmap]
rs11970716	0.80[ASN][1000 genomes]
rs1627212	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17139235	1.00[JPT][hapmap]
rs1749155	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771868	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771873	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771874	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1815673	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1815674	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1815675	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2002380	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2147705	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764128	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764131	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764133	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764140	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764144	0.90[EUR][1000 genomes]
rs2764147	0.91[EUR][1000 genomes]
rs2764150	0.83[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2764153	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764154	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764170	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764189	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793246	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2793252	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793253	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793254	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793256	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793257	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793258	0.90[EUR][1000 genomes]
rs2985677	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2994695	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2994696	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4246072	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4281005	0.89[EUR][1000 genomes]
rs59638108	0.80[ASN][1000 genomes]
rs62385113	0.88[ASN][1000 genomes]
rs62385115	0.88[ASN][1000 genomes]
rs62385117	0.88[ASN][1000 genomes]
rs62385118	0.88[ASN][1000 genomes]
rs62385119	0.88[ASN][1000 genomes]
rs62385121	0.80[ASN][1000 genomes]
rs62385122	0.80[ASN][1000 genomes]
rs726743	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754334	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs811259	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs877229	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs9328283	0.80[ASN][1000 genomes]
rs9378925	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4982400-4995000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:4982600-4995000	Weak transcription	Fetal Thymus	thymus
3	chr6:4983000-4997600	Weak transcription	Psoas Muscle	Psoas
4	chr6:4984200-4994800	Weak transcription	HepG2	liver
5	chr6:4985200-4995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:4985600-4997000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:4985600-4997000	Weak transcription	Gastric	stomach
8	chr6:4985600-5001000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:4985600-5003000	Weak transcription	HUVEC	blood vessel
10	chr6:4985600-5003200	Weak transcription	Hela-S3	cervix
11	chr6:4985800-4994800	Weak transcription	Esophagus	oesophagus
12	chr6:4985800-5003600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:4987600-5003000	Weak transcription	GM12878-XiMat	blood
14	chr6:4987600-5003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:4988000-5001400	Weak transcription	NHEK	skin
16	chr6:4988200-4994800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:4988200-4994800	Weak transcription	Brain Substantia Nigra	brain
18	chr6:4988200-5003600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:4988800-4995200	Weak transcription	Primary B cells from cord blood	blood
20	chr6:4988800-5001200	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:4988800-5001200	Weak transcription	K562	blood
22	chr6:4988800-5003600	Weak transcription	HMEC	breast
23	chr6:4989000-4995000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:4989200-5003600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:4989400-4994800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:4989400-4995800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:4989600-4995600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:4989800-4994800	Weak transcription	Adipose Nuclei	Adipose
29	chr6:4990000-4994800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:4990000-4996200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:4990000-5003600	Weak transcription	Fetal Lung	lung
32	chr6:4990200-4995000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:4990200-5001200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:4990400-4994800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr6:4990400-5001200	Weak transcription	A549	lung
36	chr6:4990400-5003600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:4990400-5003600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:4990600-4995000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:4990600-4996400	Weak transcription	Ovary	ovary
40	chr6:4990600-4996600	Weak transcription	Thymus	Thymus
41	chr6:4990800-5003000	Weak transcription	Fetal Heart	heart
42	chr6:4990800-5003600	Weak transcription	Right Ventricle	heart
43	chr6:4991000-4994800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:4991000-5002600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:4991200-4994800	Weak transcription	Fetal Kidney	kidney
46	chr6:4991200-4995000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:4991200-5002400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:4991400-4995200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:4991400-4998000	Weak transcription	Osteobl	bone
50	chr6:4991400-5001200	Weak transcription	HSMMtube	muscle

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