Variant report

Variant	rs310460
Chromosome Location	chr19:56113021-56113022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56110141-56113242	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:56109976-56113063	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:56110094-56113067	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:56112448-56113079	HUVEC	blood vessel:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55896562..55899346-chr19:56111616..56113771,2	MCF-7	breast:
2	chr19:56109995..56114029-chr19:56145200..56149074,4	MCF-7	breast:
3	chr19:55986046..55989016-chr19:56110567..56114260,3	K562	blood:
4	chr19:56111889..56113389-chr19:56150627..56153013,2	K562	blood:
5	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:
6	chr19:55789004..55791837-chr19:56110524..56113034,2	K562	blood:
7	chr19:56109378..56114662-chr19:56134412..56139001,15	K562	blood:
8	chr19:55972027..55974548-chr19:56111000..56113265,2	MCF-7	breast:
9	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
10	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
11	chr19:56110523..56113100-chr19:56152133..56154992,3	K562	blood:
12	chr19:56091409..56094452-chr19:56108819..56113428,6	K562	blood:
13	chr19:55917877..55920503-chr19:56111114..56113096,2	K562	blood:
14	chr19:56110285..56113089-chr19:56164482..56167654,4	MCF-7	breast:
15	chr19:55971482..55974428-chr19:56110628..56113037,3	K562	blood:

No data

Variant related genes	Relation type
ZNF865	TF binding region
FIZ1	TF binding region
ZNF524	TF binding region
ENSG00000063244	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000108107	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1423053	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1423054	0.92[ASN][1000 genomes]
rs2902749	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs310458	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310459	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310461	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310462	0.97[ASN][1000 genomes]
rs497264	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498199	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609075	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS 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	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 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	chr19:56111600-56116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:56112000-56113200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr19:56112200-56113200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:56112200-56113200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:56112200-56113200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr19:56112200-56113200	Flanking Active TSS	NHEK	skin
7	chr19:56112200-56113400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:56112200-56113400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr19:56112200-56116000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:56112400-56113200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:56112400-56113400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:56112400-56113600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:56112400-56113600	Enhancers	Spleen	Spleen
14	chr19:56112400-56114600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:56112400-56114600	Enhancers	Gastric	stomach
16	chr19:56112400-56116000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:56112400-56116000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:56112400-56116400	Weak transcription	Aorta	Aorta
19	chr19:56112600-56113200	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:56112600-56113200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:56112600-56113200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr19:56112600-56113200	Enhancers	Fetal Thymus	thymus
23	chr19:56112600-56113400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:56112600-56113800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:56112600-56114000	Enhancers	Placenta	Placenta
26	chr19:56112600-56115000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:56112600-56115400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr19:56112600-56116000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:56112600-56116000	Weak transcription	Fetal Lung	lung
30	chr19:56112600-56116000	Weak transcription	HSMMtube	muscle
31	chr19:56112800-56113200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr19:56112800-56113200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:56112800-56113200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:56112800-56113200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:56112800-56113200	Enhancers	Colonic Mucosa	Colon
36	chr19:56112800-56113200	Enhancers	Thymus	Thymus
37	chr19:56112800-56113200	Enhancers	A549	lung
38	chr19:56112800-56113400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr19:56112800-56113400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr19:56112800-56113400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:56112800-56113600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr19:56112800-56113600	Weak transcription	Right Ventricle	heart
43	chr19:56112800-56113800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:56112800-56113800	Enhancers	Pancreas	Pancrea
45	chr19:56112800-56114000	Weak transcription	Esophagus	oesophagus
46	chr19:56112800-56114600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:56112800-56114600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:56112800-56114600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:56112800-56114800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:56112800-56114800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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