Variant report

Variant	rs35464704
Chromosome Location	chr20:25566774-25566775
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr20:25566319-25566812	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:25566770-25566803	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25563758..25567670-chr20:25600746..25606260,10	MCF-7	breast:
2	chr20:25564265..25567754-chr20:25602950..25606854,10	MCF-7	breast:
3	chr20:25476655..25479810-chr20:25563858..25567519,3	MCF-7	breast:
4	chr20:25565180..25567156-chr20:25676091..25678288,2	MCF-7	breast:

Variant related genes	Relation type
NINL	TF binding region
ENSG00000101004	Chromatin interaction
ENSG00000130684	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11697535	0.83[AMR][1000 genomes]
rs11698047	1.00[EUR][1000 genomes]
rs13045549	0.83[AMR][1000 genomes]
rs34056528	0.83[AMR][1000 genomes]
rs35000100	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35473198	1.00[EUR][1000 genomes]
rs35705198	0.83[AMR][1000 genomes]
rs6132841	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6132843	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6132855	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138578	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6138585	0.83[AMR][1000 genomes]
rs6138638	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138642	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS 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 target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic 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	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
17	esv3436551	chr20:25564777-25567325	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv3392512	chr20:25565052-25567300	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25564800-25566800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr20:25565000-25566800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr20:25565000-25566800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr20:25565000-25566800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:25565000-25566800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:25565000-25566800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:25565000-25566800	Active TSS	Brain Anterior Caudate	brain
8	chr20:25565000-25566800	Active TSS	Fetal Kidney	kidney
9	chr20:25565000-25567000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr20:25565200-25566800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr20:25565200-25566800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr20:25565200-25566800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:25565200-25566800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr20:25565200-25566800	Active TSS	Fetal Stomach	stomach
15	chr20:25565200-25567000	Bivalent/Poised TSS	Psoas Muscle	Psoas
16	chr20:25565400-25566800	Active TSS	Fetal Brain Female	brain
17	chr20:25565600-25566800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:25565600-25566800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr20:25565600-25566800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:25565600-25566800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:25565600-25566800	Active TSS	Primary T cells from cord blood	blood
22	chr20:25565600-25566800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:25565600-25566800	Active TSS	Brain Cingulate Gyrus	brain
24	chr20:25565600-25566800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr20:25565600-25566800	Active TSS	Colon Smooth Muscle	Colon
26	chr20:25565600-25566800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr20:25565600-25566800	Active TSS	Fetal Muscle Trunk	muscle
28	chr20:25565600-25566800	Active TSS	HUVEC	blood vessel
29	chr20:25565600-25566800	Active TSS	Osteobl	bone
30	chr20:25565600-25567000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr20:25565800-25566800	Active TSS	Adipose Nuclei	Adipose
32	chr20:25566000-25566800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr20:25566000-25566800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr20:25566000-25566800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr20:25566000-25566800	Active TSS	Stomach Smooth Muscle	stomach
36	chr20:25566200-25566800	Active TSS	Brain Germinal Matrix	brain
37	chr20:25566200-25566800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr20:25566400-25566800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr20:25566400-25566800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr20:25566400-25566800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr20:25566400-25566800	Flanking Active TSS	Fetal Thymus	thymus
42	chr20:25566400-25566800	Flanking Active TSS	Thymus	Thymus
43	chr20:25566400-25566800	Flanking Active TSS	A549	lung
44	chr20:25566400-25566800	Flanking Active TSS	HepG2	liver
45	chr20:25566600-25566800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
46	chr20:25566600-25566800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25566600-25566800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr20:25566600-25566800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr20:25566600-25566800	Active TSS	Primary hematopoietic stem cells	blood
50	chr20:25566600-25566800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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