Variant report

Variant	rs56049414
Chromosome Location	chr15:51261970-51261971
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs16963979	1.00[AMR][1000 genomes]
rs28865017	1.00[AMR][1000 genomes]
rs55683982	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735813	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55742119	1.00[AMR][1000 genomes]
rs55763666	1.00[AMR][1000 genomes]
rs55912100	1.00[AMR][1000 genomes]
rs55920356	1.00[AMR][1000 genomes]
rs55940433	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55973448	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56010315	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56017509	1.00[AMR][1000 genomes]
rs56046825	1.00[AMR][1000 genomes]
rs56056949	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56121717	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56222335	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56273151	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56283133	1.00[AMR][1000 genomes]
rs56289716	1.00[AMR][1000 genomes]
rs56374503	1.00[AMR][1000 genomes]
rs56813592	1.00[AMR][1000 genomes]
rs57221782	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57305511	1.00[AMR][1000 genomes]
rs57499524	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57831362	1.00[AMR][1000 genomes]
rs57949904	1.00[AMR][1000 genomes]
rs58651255	1.00[AMR][1000 genomes]
rs59067851	1.00[AMR][1000 genomes]
rs59155793	1.00[AMR][1000 genomes]
rs59364110	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59681404	1.00[AMR][1000 genomes]
rs59843670	1.00[AMR][1000 genomes]
rs59865784	1.00[AMR][1000 genomes]
rs60037205	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60253924	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60297574	1.00[AMR][1000 genomes]
rs60700183	1.00[AMR][1000 genomes]
rs60775199	1.00[AMR][1000 genomes]
rs61106666	1.00[AMR][1000 genomes]
rs61698311	1.00[AMR][1000 genomes]
rs6493467	1.00[AMR][1000 genomes]
rs7171301	1.00[AMR][1000 genomes]
rs7174066	1.00[AMR][1000 genomes]
rs7175547	1.00[AMR][1000 genomes]
rs74012820	1.00[AMR][1000 genomes]
rs74012821	1.00[AMR][1000 genomes]
rs74013114	1.00[AMR][1000 genomes]
rs74013115	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013125	1.00[AMR][1000 genomes]
rs74013127	1.00[AMR][1000 genomes]
rs74013128	1.00[AMR][1000 genomes]
rs74013130	1.00[AMR][1000 genomes]
rs74013132	1.00[AMR][1000 genomes]
rs74015214	1.00[AMR][1000 genomes]
rs74015215	1.00[AMR][1000 genomes]
rs74015226	1.00[AMR][1000 genomes]
rs74015228	1.00[AMR][1000 genomes]
rs74015229	1.00[AMR][1000 genomes]
rs74015230	1.00[AMR][1000 genomes]
rs74015232	1.00[AMR][1000 genomes]
rs74015235	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015236	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
3	chr15:51235200-51263800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:51243800-51283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:51250400-51264800	Weak transcription	NHEK	skin
6	chr15:51252200-51262400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:51252200-51263400	Weak transcription	NHLF	lung
8	chr15:51252400-51283800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:51253400-51265600	Weak transcription	HMEC	breast
10	chr15:51253600-51262200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:51253800-51262200	Weak transcription	NHDF-Ad	bronchial
12	chr15:51253800-51262400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:51253800-51262400	Weak transcription	NH-A	brain
14	chr15:51255800-51263200	Weak transcription	HUVEC	blood vessel
15	chr15:51257200-51262800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:51257400-51262400	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:51257600-51262000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:51257600-51262000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:51257600-51262200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:51257600-51262200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:51257600-51264800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:51257600-51264800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:51257600-51272800	Weak transcription	Pancreas	Pancrea
24	chr15:51257800-51262600	Weak transcription	Psoas Muscle	Psoas
25	chr15:51257800-51262800	Weak transcription	Right Ventricle	heart
26	chr15:51257800-51263000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:51257800-51264600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:51258000-51262400	Weak transcription	Brain Substantia Nigra	brain
29	chr15:51258000-51262800	Weak transcription	HSMMtube	muscle
30	chr15:51258000-51263200	Weak transcription	Small Intestine	intestine
31	chr15:51258200-51262800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:51259400-51262200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:51259400-51262600	Weak transcription	HepG2	liver
34	chr15:51259400-51264000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:51259400-51264400	Strong transcription	Osteobl	bone
36	chr15:51259600-51262200	Strong transcription	Primary T cells from cord blood	blood
37	chr15:51259600-51262200	Weak transcription	Brain Anterior Caudate	brain
38	chr15:51259600-51262400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:51259600-51263000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:51259600-51263600	Strong transcription	Ovary	ovary
41	chr15:51259600-51265200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr15:51259800-51267000	Strong transcription	Placenta	Placenta
43	chr15:51260000-51262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:51260000-51262200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:51260000-51262200	Strong transcription	Left Ventricle	heart
46	chr15:51260000-51262200	Strong transcription	Thymus	Thymus
47	chr15:51260000-51262400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:51260200-51262000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:51260200-51262200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:51260400-51262200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood

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