Variant report

Variant	rs35000100
Chromosome Location	chr20:25605223-25605224
allele	A/C/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	POLR2A	chr20:25603743-25605454	Hela-S3	cervix:	n/a	n/a
2	CEBPD	chr20:25604204-25605307	HepG2	liver:	n/a	n/a
3	YY1	chr20:25604239-25605284	GM12891	blood:	n/a	chr20:25604387-25604401 chr20:25604616-25604630 chr20:25604348-25604359 chr20:25604390-25604404 chr20:25605267-25605276
4	E2F4	chr20:25603954-25605528	K562	blood:	n/a	chr20:25604629-25604638 chr20:25604596-25604607 chr20:25605119-25605134 chr20:25604394-25604404 chr20:25605116-25605128
5	JUND	chr20:25604284-25605347	K562	blood:	n/a	n/a
6	MAZ	chr20:25603686-25605342	GM12878	blood:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
7	MAX	chr20:25603603-25605486	K562	blood:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
8	GATA3	chr20:25604150-25605341	MCF-7	breast:	n/a	n/a
9	POLR2A	chr20:25603585-25605618	HepG2	liver:	n/a	n/a
10	TEAD4	chr20:25604352-25605300	ECC-1	luminal epithelium:	n/a	n/a
11	TAF7	chr20:25604582-25605272	H1-hESC	embryonic stem cell:	n/a	n/a
12	BACH1	chr20:25605186-25605431	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr20:25605210-25605466	HepG2	liver:	n/a	n/a
14	ZNF263	chr20:25604448-25605376	HEK293-T-REx	kidney:	n/a	chr20:25604662-25604671
15	CHD1	chr20:25603826-25605423	GM12878	blood:	n/a	chr20:25605122-25605132 chr20:25604442-25604452
16	TEAD4	chr20:25604471-25605281	K562	blood:	n/a	n/a
17	JUND	chr20:25604426-25605249	H1-hESC	embryonic stem cell:	n/a	n/a
18	SIN3AK20	chr20:25603787-25605260	A549	lung:	n/a	n/a
19	POLR2A	chr20:25604029-25605249	A549	lung:	n/a	n/a
20	KAP1	chr20:25604306-25605304	U2OS	brain:	n/a	n/a
21	POLR2A	chr20:25603725-25605447	GM12892	blood:	n/a	n/a
22	POU2F2	chr20:25604157-25605274	GM12878	blood:	n/a	n/a
23	POLR2A	chr20:25603865-25605348	MCF-7	breast:	n/a	n/a
24	BRCA1	chr20:25604003-25605491	HepG2	liver:	n/a	n/a
25	MAX	chr20:25603605-25605490	K562	blood:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
26	MAFK	chr20:25605084-25605262	K562	blood:	n/a	n/a
27	EP300	chr20:25603635-25605255	GM12878	blood:	n/a	chr20:25604388-25604404 chr20:25604587-25604596 chr20:25604183-25604199
28	MAX	chr20:25603669-25605523	Hela-S3	cervix:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
29	YY1	chr20:25604345-25605292	SK-N-SH_RA	brain:	n/a	chr20:25604387-25604401 chr20:25604616-25604630 chr20:25604348-25604359 chr20:25604390-25604404 chr20:25605267-25605276
30	TCF7L2	chr20:25605137-25605271	PANC-1	pancreas:	n/a	n/a
31	MAFK	chr20:25604568-25605341	HepG2	liver:	n/a	n/a
32	POLR2A	chr20:25603715-25605523	GM19099	blood:	n/a	n/a
33	MAX	chr20:25603644-25605557	MCF-7	breast:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
34	POLR2A	chr20:25604290-25605329	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr20:25603391-25605382	Hela-S3	cervix:	n/a	n/a
36	EP300	chr20:25603876-25605496	HepG2	liver:	n/a	chr20:25604388-25604404 chr20:25604587-25604596 chr20:25604183-25604199
37	POLR2A	chr20:25603762-25605409	GM18505	blood:	n/a	n/a
38	PML	chr20:25603786-25605377	MCF-7	breast:	n/a	n/a
39	MYC	chr20:25603644-25605411	MCF10A-Er-Src	breast:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
40	POLR2A	chr20:25604054-25605413	K562	blood:	n/a	n/a
41	MAX	chr20:25603608-25605603	HepG2	liver:	n/a	chr20:25603913-25603922 chr20:25603913-25603922
42	ZBTB33	chr20:25604072-25605371	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr20:25604219-25605593	K562	blood:	n/a	n/a
44	TEAD4	chr20:25604477-25605366	A549	lung:	n/a	n/a
45	POLR2A	chr20:25603781-25605443	MCF-7	breast:	n/a	n/a
46	POLR2A	chr20:25603748-25605308	GM12878	blood:	n/a	n/a
47	BRCA1	chr20:25604006-25605244	GM12878	blood:	n/a	n/a
48	ATF3	chr20:25604408-25605384	A549	lung:	n/a	chr20:25604441-25604450
49	CREB1	chr20:25604051-25605265	A549	lung:	n/a	n/a
50	POLR2A	chr20:25604304-25605292	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25605178-25605228	NHBE	bronchial:	n/a
2	chr20:25605178-25605228	AG09319	gingival:	n/a
3	chr20:25605178-25605228	SK-N-SH	brain:	n/a
4	chr20:25605178-25605228	PANC-1	pancreas:	n/a
5	chr20:25605178-25605228	SAEC	small airway:	n/a
6	chr20:25605178-25605228	GM12892	blood:	n/a
7	chr20:25605178-25605228	RPTEC	kidney:	n/a
8	chr20:25605178-25605228	SKMC	muscle:	n/a
9	chr20:25605178-25605228	NH-A	brain:	n/a
10	chr20:25605178-25605228	AG04449	skin:	fetal
11	chr20:25605178-25605228	HCT-116	colon:	n/a
12	chr20:25605178-25605228	SK-N-SH_RA	brain:	n/a
13	chr20:25605178-25605228	ProgFib	skin:	n/a
14	chr20:25605178-25605228	HRE	kidney:	n/a
15	chr20:25605178-25605228	HCM	heart:	n/a
16	chr20:25605178-25605228	PFSK-1	brain:	n/a
17	chr20:25605178-25605228	AoSMC	blood vessel:	n/a
18	chr20:25605178-25605228	MCF-7	breast:	n/a
19	chr20:25605178-25605228	GM19239	blood:	n/a
20	chr20:25605178-25605228	H1-hESC	embryonic stem cell:	embryo
21	chr20:25605178-25605228	HUVEC	blood vessel:	n/a
22	chr20:25605178-25605228	HRPEpiC	eye:	n/a
23	chr20:25605178-25605228	HAEpiC	amniotic membrane:	n/a
24	chr20:25605178-25605228	ECC-1	luminal epithelium:	n/a
25	chr20:25605178-25605228	HepG2	liver:	n/a
26	chr20:25605178-25605228	GM06990	blood:	n/a
27	chr20:25605178-25605228	AG09309	skin:	n/a
28	chr20:25605178-25605228	BE2_C	brain:	n/a
29	chr20:25605178-25605228	HL-60	blood:	n/a
30	chr20:25605178-25605228	BJ	skin:	n/a
31	chr20:25605178-25605228	HIPEpiC	eye:	n/a
32	chr20:25605178-25605228	LNCaP	prostate:	n/a
33	chr20:25605178-25605228	A549	lung:	n/a
34	chr20:25605178-25605228	PrEC	prostate:	n/a
35	chr20:25605178-25605228	NHDF-neo	bronchial:	n/a
36	chr20:25605178-25605228	Jurkat	blood:	n/a
37	chr20:25605178-25605228	Hela-S3	cervix:	n/a
38	chr20:25605178-25605228	HEEpiC	esophagus:	n/a
39	chr20:25605178-25605228	HMEC	breast:	n/a
40	chr20:25605178-25605228	HCF	heart:	n/a
41	chr20:25605178-25605228	NT2-D1	testis:	n/a
42	chr20:25605178-25605228	SK-N-MC	brain:	n/a
43	chr20:25605178-25605228	GM12891	blood:	n/a
44	chr20:25605178-25605228	HNPCEpiC	eye:	n/a
45	chr20:25605178-25605228	U87	brain:	n/a
46	chr20:25605178-25605228	K562	blood:	n/a
47	chr20:25605178-25605228	Caco-2	colon:	n/a
48	chr20:25605178-25605228	Hepatocyte	liver:	n/a
49	chr20:25605178-25605228	HPAEpiC	pulmonary alveolar:	n/a
50	chr20:25605178-25605228	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25563758..25567670-chr20:25600746..25606260,10	MCF-7	breast:
2	chr20:25604862..25606415-chr20:25633775..25635785,2	MCF-7	breast:
3	chr20:25590781..25592605-chr20:25602144..25606440,3	MCF-7	breast:
4	chr20:25603699..25606216-chr20:25676779..25679090,3	MCF-7	breast:
5	chr20:25564265..25567754-chr20:25602950..25606854,10	MCF-7	breast:
6	chr20:25474956..25477524-chr20:25604184..25606432,2	MCF-7	breast:
7	chr20:25601566..25607773-chr20:25608657..25615631,12	MCF-7	breast:
8	chr20:25604068..25607059-chr20:25675582..25678596,4	MCF-7	breast:
9	chr20:25571499..25573188-chr20:25604906..25607655,2	K562	blood:
10	chr20:25602422..25607796-chr20:25675112..25679388,9	K562	blood:
11	chr20:24972575..24975462-chr20:25603621..25605250,2	K562	blood:
12	chr20:25475529..25477645-chr20:25603569..25606189,3	MCF-7	breast:
13	chr20:25604700..25606724-chr20:25650561..25652560,2	MCF-7	breast:
14	chr20:25604858..25606778-chr20:25612734..25614672,2	MCF-7	breast:
15	chr20:25591410..25597359-chr20:25600309..25606040,12	K562	blood:
16	chr20:25603625..25606406-chr20:25665177..25670447,5	MCF-7	breast:
17	chr20:25602965..25606226-chr20:25676160..25678613,3	K562	blood:

Variant related genes	Relation type
NANP	TF binding region
NANP	CpG island
ENSG00000101474	Chromatin interaction
ENSG00000242236	Chromatin interaction
ENSG00000236542	Chromatin interaction
ENSG00000130684	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000101004	Chromatin interaction
ENSG00000251883	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11698047	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35464704	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]
rs6132855	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138578	1.00[AFR][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:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25603000-25606000	Active TSS	K562	blood
2	chr20:25603200-25605600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:25603200-25605600	Active TSS	Fetal Intestine Small	intestine
4	chr20:25603200-25605800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:25603400-25605400	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr20:25603400-25605400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr20:25603400-25605400	Active TSS	Ovary	ovary
8	chr20:25603400-25605600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr20:25603400-25605600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr20:25603400-25605600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr20:25603400-25605600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr20:25603400-25605600	Active TSS	Fetal Lung	lung
13	chr20:25603400-25605600	Active TSS	HSMM	muscle
14	chr20:25603400-25606600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:25603600-25605400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:25603600-25605400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr20:25603600-25605400	Active TSS	Aorta	Aorta
18	chr20:25603600-25605400	Active TSS	Gastric	stomach
19	chr20:25603600-25605600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr20:25603600-25605600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr20:25603600-25605600	Active TSS	Colon Smooth Muscle	Colon
22	chr20:25603600-25605600	Active TSS	Fetal Kidney	kidney
23	chr20:25603600-25605600	Active TSS	Rectal Smooth Muscle	rectum
24	chr20:25603600-25605600	Active TSS	Osteobl	bone
25	chr20:25603600-25605800	Active TSS	Hela-S3	cervix
26	chr20:25603600-25606200	Active TSS	A549	lung
27	chr20:25603800-25605400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr20:25603800-25605400	Active TSS	Brain Anterior Caudate	brain
29	chr20:25603800-25605400	Active TSS	Small Intestine	intestine
30	chr20:25603800-25605600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr20:25603800-25605600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr20:25603800-25605600	Active TSS	Brain Hippocampus Middle	brain
33	chr20:25603800-25605600	Active TSS	Brain Substantia Nigra	brain
34	chr20:25603800-25605600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr20:25603800-25605600	Active TSS	Thymus	Thymus
36	chr20:25604000-25605400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:25604000-25605400	Active TSS	Fetal Brain Male	brain
38	chr20:25604000-25605600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr20:25604000-25605600	Active TSS	Fetal Brain Female	brain
40	chr20:25604000-25605800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr20:25604200-25605600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr20:25604200-25605600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr20:25604200-25605600	Active TSS	Primary T cells from cord blood	blood
44	chr20:25604200-25605600	Active TSS	Colonic Mucosa	Colon
45	chr20:25604600-25605400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
46	chr20:25604600-25605800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:25604800-25605400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr20:25604800-25605400	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr20:25604800-25605400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr20:25604800-25605600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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