Variant report

Variant	rs1589816
Chromosome Location	chr7:64454557-64454558
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr7:64454525-64454943	H1-hESC	embryonic stem cell:	n/a	chr7:64454712-64454724
2	POLR2A	chr7:64450474-64460656	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:64430037..64431649-chr7:64452828..64455445,2	K562	blood:
2	chr7:64454254..64456313-chr7:64461588..64463647,2	MCF-7	breast:
3	chr7:64453338..64456420-chr7:64456552..64459818,7	K562	blood:
4	chr7:64454048..64457765-chr7:64465398..64467279,3	MCF-7	breast:
5	chr7:64414429..64416798-chr7:64452211..64454777,2	MCF-7	breast:
6	chr7:64452604..64455149-chr7:64456846..64459558,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF117	TF binding region
ENSG00000213462	Chromatin interaction
ENSG00000152926	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10241221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10253907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10268911	0.90[AMR][1000 genomes]
rs10277801	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1060382	0.81[AFR][1000 genomes]
rs10807685	0.84[AFR][1000 genomes]
rs10807688	0.80[AMR][1000 genomes]
rs11972247	0.84[AFR][1000 genomes]
rs11978819	0.84[AFR][1000 genomes]
rs12234848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12334031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13222878	0.83[AFR][1000 genomes]
rs13229671	0.89[AFR][1000 genomes]
rs13229816	0.89[AFR][1000 genomes]
rs13230970	0.81[AFR][1000 genomes]
rs1404453	0.81[AFR][1000 genomes]
rs1524821	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1568819	0.80[AMR][1000 genomes]
rs1608712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1608713	0.81[AFR][1000 genomes]
rs1608716	0.81[AFR][1000 genomes]
rs1608717	0.99[AFR][1000 genomes]
rs1709519	0.80[AMR][1000 genomes]
rs1852015	0.81[AFR][1000 genomes]
rs1852016	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1970879	0.81[AFR][1000 genomes]
rs1971427	0.83[AFR][1000 genomes]
rs1972156	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2049441	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2177660	0.89[AFR][1000 genomes]
rs28411715	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34216774	0.83[AFR][1000 genomes]
rs4422675	0.80[AMR][1000 genomes]
rs4618579	0.99[AFR][1000 genomes]
rs4717229	0.99[AFR][1000 genomes]
rs4718173	0.81[AFR][1000 genomes]
rs4718174	0.81[AFR][1000 genomes]
rs4718175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4718176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4718179	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4718184	0.82[AFR][1000 genomes]
rs6460215	0.82[AFR][1000 genomes]
rs6460219	0.99[AFR][1000 genomes]
rs6460220	0.90[AFR][1000 genomes]
rs6460223	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6944240	0.81[AFR][1000 genomes]
rs6949548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7781025	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7784273	0.89[AFR][1000 genomes]
rs7784866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7789630	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7790578	0.81[AFR][1000 genomes]
rs7790622	0.80[AMR][1000 genomes]
rs7796144	0.99[AFR][1000 genomes]
rs7799463	0.81[AFR][1000 genomes]
rs7803418	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7810102	0.81[AFR][1000 genomes]
rs7812013	0.84[AFR][1000 genomes]
rs940588	0.81[AFR][1000 genomes]
rs9638214	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9638416	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active 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	59 gene(s)	inside rSNPs	diseases
2	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1019180	chr7:64329889-64512842	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv888283	chr7:64343985-64511564	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv2752165	chr7:64345822-65208605	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv888284	chr7:64406439-64562139	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv970505	chr7:64441807-64494987	ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1033517	chr7:64443052-64942418	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv538893	chr7:64443052-64942418	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	esv3346218	chr7:64450915-64459952	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64433400-64465600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:64438600-64465200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:64440200-64457600	Weak transcription	Pancreas	Pancrea
4	chr7:64441800-64456800	Weak transcription	Fetal Heart	heart
5	chr7:64441800-64459400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:64441800-64465000	Weak transcription	Brain Angular Gyrus	brain
7	chr7:64442000-64457600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:64443800-64457200	Weak transcription	Right Ventricle	heart
9	chr7:64446000-64460000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr7:64448800-64461200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:64449000-64465200	ZNF genes & repeats	Fetal Brain Female	brain
12	chr7:64450000-64464000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr7:64450200-64460000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:64450200-64460000	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr7:64450200-64460000	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr7:64450200-64462400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:64450200-64462400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:64450200-64462600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:64450200-64465400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:64450400-64455400	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr7:64450400-64460000	ZNF genes & repeats	Placenta	Placenta
22	chr7:64450400-64460200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr7:64450400-64464000	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr7:64450400-64464400	ZNF genes & repeats	Dnd41	blood
25	chr7:64450600-64460000	ZNF genes & repeats	Fetal Stomach	stomach
26	chr7:64450600-64462400	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr7:64451000-64455000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:64451200-64465400	Weak transcription	Brain Substantia Nigra	brain
29	chr7:64451400-64454800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:64451800-64454600	Strong transcription	Adipose Nuclei	Adipose
31	chr7:64451800-64454800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:64452000-64464600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:64452200-64454600	ZNF genes & repeats	Thymus	Thymus
34	chr7:64453600-64454800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:64453600-64457800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:64453800-64457400	Weak transcription	Left Ventricle	heart
37	chr7:64453800-64457400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr7:64453800-64457800	Weak transcription	HSMMtube	muscle
39	chr7:64453800-64459000	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:64453800-64459200	Weak transcription	Gastric	stomach
41	chr7:64453800-64465200	Weak transcription	Brain Anterior Caudate	brain
42	chr7:64453800-64465400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr7:64453800-64465400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:64454000-64457800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:64454000-64459200	Weak transcription	Ovary	ovary
46	chr7:64454000-64459200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:64454400-64458400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links