Variant report

Variant	rs55742119
Chromosome Location	chr15:51293644-51293645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51293258..51295626-chr15:51337830..51340357,2	MCF-7	breast:
2	chr15:51288949..51290565-chr15:51293447..51295234,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs16963979	1.00[AMR][1000 genomes]
rs28865017	1.00[AMR][1000 genomes]
rs55683982	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735813	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55763666	1.00[AMR][1000 genomes]
rs55912100	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55920356	0.86[AFR][1000 genomes];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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56049414	1.00[AMR][1000 genomes]
rs56056949	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56121717	0.91[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57221782	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57305511	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57322405	0.88[AFR][1000 genomes]
rs57499524	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57831362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57949904	1.00[AMR][1000 genomes]
rs58651255	1.00[AMR][1000 genomes]
rs58652891	0.81[AFR][1000 genomes]
rs58853092	0.84[AFR][1000 genomes]
rs59067851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59155793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59364110	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59681404	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59843670	0.94[AFR][1000 genomes];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	0.94[AFR][1000 genomes];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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013128	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013132	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013134	0.88[AFR][1000 genomes]
rs74013136	0.88[AFR][1000 genomes]
rs74013140	0.84[AFR][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:14 , 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	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
7	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
8	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
9	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
10	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
11	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
14	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 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	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
2	chr15:51261600-51295600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:51261600-51298200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:51263000-51304800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:51263600-51296400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:51263600-51297800	Weak transcription	NHLF	lung
7	chr15:51263600-51299200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:51263600-51300200	Weak transcription	Small Intestine	intestine
9	chr15:51263600-51301200	Weak transcription	HepG2	liver
10	chr15:51263600-51303000	Weak transcription	HUVEC	blood vessel
11	chr15:51263800-51296200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:51263800-51296600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:51263800-51300400	Weak transcription	Right Ventricle	heart
14	chr15:51264400-51294200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:51264600-51296600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:51265200-51296400	Weak transcription	Brain Germinal Matrix	brain
17	chr15:51265200-51302400	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:51265200-51315600	Weak transcription	Gastric	stomach
19	chr15:51265400-51302400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:51267000-51302200	Weak transcription	Fetal Brain Female	brain
21	chr15:51267600-51296400	Weak transcription	Fetal Brain Male	brain
22	chr15:51267800-51296400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:51270200-51302600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:51270200-51317600	Weak transcription	Psoas Muscle	Psoas
25	chr15:51273000-51296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:51273400-51296400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:51273400-51296400	Weak transcription	Esophagus	oesophagus
28	chr15:51273400-51298000	Weak transcription	Lung	lung
29	chr15:51273400-51302200	Weak transcription	Colonic Mucosa	Colon
30	chr15:51273400-51302400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:51273600-51296800	Weak transcription	Spleen	Spleen
32	chr15:51273600-51298200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:51273600-51307600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:51274200-51301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:51276400-51300600	Weak transcription	A549	lung
36	chr15:51276600-51295800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:51280800-51295400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:51281600-51295400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:51281800-51294200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:51282000-51304000	Weak transcription	Fetal Heart	heart
41	chr15:51282600-51301000	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:51283400-51294600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:51283400-51294600	Weak transcription	Thymus	Thymus
44	chr15:51283400-51296200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:51283400-51296400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:51283400-51296400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:51283400-51296400	Weak transcription	Aorta	Aorta
48	chr15:51283400-51296400	Weak transcription	Pancreas	Pancrea
49	chr15:51283400-51300400	Weak transcription	Fetal Intestine Small	intestine
50	chr15:51283600-51299600	Weak transcription	Brain Substantia Nigra	brain

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