Variant report

Variant	rs6087306
Chromosome Location	chr20:29641482-29641483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:29641433-29642137	K562	blood:	n/a	n/a
2	MXI1	chr20:29641449-29641635	K562	blood:	n/a	n/a
3	POLR2A	chr20:29641457-29641626	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF384	chr20:29641444-29641628	GM12878	blood:	n/a	n/a
5	TCF7L2	chr20:29641328-29641798	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:29640916..29641744-chr4:190895394..190895909,2	MCF-7	breast:
2	chr20:29637719..29639568-chr20:29640126..29641910,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FRG1B-1	chr20:29641421-29641792	ENSG00000223346

No data

Variant related genes	Relation type
MLLT10P1	TF binding region
ENSG00000238151	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4892328	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6057378	0.83[EUR][1000 genomes]
rs6057406	0.82[ASN][1000 genomes]
rs6118923	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6141218	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8117830	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758518	chr20:29419570-29653908	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2758791	chr20:29419570-29653908	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428028	chr20:29419570-29653908	Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv428376	chr20:29419570-29653908	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1058387	chr20:29479828-29651199	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1067193	chr20:29525410-29651199	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv11674	chr20:29528011-29653880	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv965870	chr20:29570138-29652376	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv15335	chr20:29580700-29653880	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv585870	chr20:29603773-29648195	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv585871	chr20:29612406-29648195	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv585872	chr20:29612406-29648263	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv585873	chr20:29616742-29651821	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv821487	chr20:29629343-29652652	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv828711	chr20:29629343-29652652	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv585874	chr20:29633277-29651821	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv7214	chr20:29638542-29641660	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv436321	chr20:29638637-29645554	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3420645	chr20:29638675-29641488	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv3419758	chr20:29638695-29641497	Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv3446706	chr20:29638696-29641520	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:29638800-29641600	Weak transcription	Brain Substantia Nigra	brain
2	chr20:29638800-29641800	Weak transcription	Placenta	Placenta
3	chr20:29639000-29641800	Weak transcription	Aorta	Aorta
4	chr20:29639000-29641800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr20:29640400-29641600	Weak transcription	Lung	lung
6	chr20:29641200-29641600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr20:29641200-29641800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr20:29641200-29642000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr20:29641200-29642000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr20:29641200-29642200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:29641200-29642200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
12	chr20:29641200-29642200	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr20:29641200-29642200	ZNF genes & repeats	Fetal Lung	lung
14	chr20:29641200-29643000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr20:29641400-29641600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr20:29641400-29641600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:29641400-29641600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
18	chr20:29641400-29641600	ZNF genes & repeats	NHDF-Ad	bronchial
19	chr20:29641400-29641800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:29641400-29641800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
21	chr20:29641400-29641800	ZNF genes & repeats	NH-A	brain
22	chr20:29641400-29642000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:29641400-29642000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:29641400-29642000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
25	chr20:29641400-29642000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
26	chr20:29641400-29642000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
27	chr20:29641400-29642000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr20:29641400-29642000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr20:29641400-29642000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
30	chr20:29641400-29642000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
31	chr20:29641400-29642000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:29641400-29642000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
33	chr20:29641400-29642000	ZNF genes & repeats	Brain Angular Gyrus	brain
34	chr20:29641400-29642000	ZNF genes & repeats	Brain Anterior Caudate	brain
35	chr20:29641400-29642000	ZNF genes & repeats	Colon Smooth Muscle	Colon
36	chr20:29641400-29642000	ZNF genes & repeats	Fetal Heart	heart
37	chr20:29641400-29642000	ZNF genes & repeats	Fetal Kidney	kidney
38	chr20:29641400-29642000	ZNF genes & repeats	Ovary	ovary
39	chr20:29641400-29642000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
40	chr20:29641400-29642000	ZNF genes & repeats	Stomach Mucosa	stomach
41	chr20:29641400-29642000	ZNF genes & repeats	A549	lung
42	chr20:29641400-29642000	ZNF genes & repeats	Dnd41	blood
43	chr20:29641400-29642000	ZNF genes & repeats	GM12878-XiMat	blood
44	chr20:29641400-29642000	ZNF genes & repeats	HepG2	liver
45	chr20:29641400-29642000	ZNF genes & repeats	HSMM	muscle
46	chr20:29641400-29642000	ZNF genes & repeats	HUVEC	blood vessel
47	chr20:29641400-29642000	ZNF genes & repeats	K562	blood
48	chr20:29641400-29642200	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr20:29641400-29642200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr20:29641400-29642200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links