Variant report

Variant	rs58560061
Chromosome Location	chr19:21950179-21950180
allele	C/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	CREB1	chr19:21949870-21950621	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:21949855-21950637	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:21949982-21950586	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:21950105-21950465	Hela-S3	cervix:	n/a	n/a
5	CUX1	chr19:21949945-21950705	K562	blood:	n/a	n/a
6	MAX	chr19:21949865-21950565	K562	blood:	n/a	n/a
7	CEBPB	chr19:21950045-21950640	K562	blood:	n/a	n/a
8	MAZ	chr19:21949927-21950634	HepG2	liver:	n/a	n/a
9	STAT3	chr19:21950060-21950512	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr19:21950087-21950487	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr19:21950091-21950572	SK-N-SH	brain:	n/a	n/a
12	FOS	chr19:21950154-21950637	K562	blood:	n/a	chr19:21950345-21950359
13	GABPA	chr19:21950152-21950685	SK-N-SH	brain:	n/a	n/a
14	MAX	chr19:21950104-21950502	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:21949954-21950639	MCF-7	breast:	n/a	n/a
16	POLR2A	chr19:21949933-21950631	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr19:21949839-21950475	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr19:21949915-21950585	K562	blood:	n/a	n/a
19	POLR2A	chr19:21949811-21950617	GM12878	blood:	n/a	n/a
20	TAF1	chr19:21950023-21950581	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr19:21949647-21950588	K562	blood:	n/a	n/a
22	BHLHE40	chr19:21949896-21950532	GM12878	blood:	n/a	n/a
23	SIN3A	chr19:21949792-21950536	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:21950111-21950564	HCT-116	colon:	n/a	n/a
25	ARID3A	chr19:21950050-21950688	HepG2	liver:	n/a	n/a
26	CTBP2	chr19:21949936-21950568	H1-hESC	embryonic stem cell:	n/a	n/a
27	NFIC	chr19:21949970-21950350	GM12878	blood:	n/a	n/a
28	HCFC1	chr19:21949905-21950559	K562	blood:	n/a	n/a
29	POLR2A	chr19:21950082-21950562	K562	blood:	n/a	n/a
30	UBTF	chr19:21949872-21950364	K562	blood:	n/a	n/a
31	MYC	chr19:21949920-21950672	NB4	blood:	n/a	n/a
32	MYC	chr19:21949755-21950590	K562	blood:	n/a	n/a
33	TCF7L2	chr19:21950125-21950501	Hela-S3	cervix:	n/a	n/a
34	TAF1	chr19:21949814-21950560	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:21949719-21950596	MCF10A-Er-Src	breast:	n/a	n/a
36	BHLHE40	chr19:21949802-21950565	K562	blood:	n/a	n/a
37	YY1	chr19:21949892-21950230	HCT-116	colon:	n/a	chr19:21950064-21950075 chr19:21950071-21950093 chr19:21950072-21950080 chr19:21950059-21950073 chr19:21950071-21950081
38	HEY1	chr19:21950016-21950616	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:21949869-21950513	K562	blood:	n/a	n/a
40	POLR2A	chr19:21949782-21950592	GM12878	blood:	n/a	n/a
41	GABPA	chr19:21950090-21950681	HL-60	blood:	n/a	n/a
42	JUN	chr19:21950150-21950603	K562	blood:	n/a	chr19:21950345-21950359
43	PML	chr19:21949990-21950571	K562	blood:	n/a	n/a
44	YY1	chr19:21949732-21950441	H1-hESC	embryonic stem cell:	n/a	chr19:21950064-21950075 chr19:21950071-21950093 chr19:21950072-21950080 chr19:21950059-21950073 chr19:21950071-21950081
45	CTCF	chr19:21949884-21950193	Fibrobl	skin:	n/a	chr19:21950065-21950086 chr19:21950070-21950088
46	POLR2A	chr19:21949818-21950611	HL-60	blood:	n/a	n/a
47	YY1	chr19:21949856-21950533	SK-N-SH_RA	brain:	n/a	chr19:21950064-21950075 chr19:21950071-21950093 chr19:21950072-21950080 chr19:21950059-21950073 chr19:21950071-21950081
48	SIN3AK20	chr19:21949880-21950619	SK-N-SH	brain:	n/a	n/a
49	YY1	chr19:21949563-21950645	SK-N-SH	brain:	n/a	chr19:21950064-21950075 chr19:21950071-21950093 chr19:21950072-21950080 chr19:21950059-21950073 chr19:21950071-21950081
50	EP300	chr19:21949796-21950656	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:21948377..21950622-chr19:22016631..22019164,2	MCF-7	breast:
2	chr19:21950144..21952867-chr19:22033592..22036117,2	MCF-7	breast:
3	chr19:21948493..21950510-chr19:22018479..22020127,2	MCF-7	breast:

Variant related genes	Relation type
ZNF100	TF binding region
ENSG00000198521	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs57484704	1.00[AMR][1000 genomes]
rs61467203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250493	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3392559	chr19:21798396-21965956	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv833783	chr19:21821406-21991838	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1815274	chr19:21825750-21981855	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv911426	chr19:21892040-21973929	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv911427	chr19:21900898-21960407	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv833784	chr19:21902647-22037153	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv578970	chr19:21906655-21973929	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv961193	chr19:21911308-21950500	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv3342879	chr19:21913482-21968857	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1059457	chr19:21940891-21999025	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21948400-21950600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:21948600-21950200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:21948600-21950600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:21948600-21950600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:21948600-21950600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:21948600-21950600	Active TSS	Fetal Kidney	kidney
7	chr19:21948600-21950800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:21948600-21950800	Active TSS	Right Atrium	heart
9	chr19:21948600-21951200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:21948800-21950800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:21948800-21950800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:21949000-21950600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:21949000-21950600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:21949000-21950600	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr19:21949000-21950600	Active TSS	Brain Hippocampus Middle	brain
16	chr19:21949000-21950600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr19:21949000-21950600	Active TSS	HMEC	breast
18	chr19:21949000-21950600	Active TSS	HUVEC	blood vessel
19	chr19:21949000-21950800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:21949000-21950800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:21949000-21950800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr19:21949000-21950800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr19:21949000-21950800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:21949000-21950800	Active TSS	Fetal Brain Female	brain
25	chr19:21949000-21950800	Active TSS	Stomach Smooth Muscle	stomach
26	chr19:21949000-21950800	Active TSS	GM12878-XiMat	blood
27	chr19:21949200-21950400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:21949200-21950400	Active TSS	Fetal Muscle Leg	muscle
29	chr19:21949200-21950400	Active TSS	Placenta	Placenta
30	chr19:21949200-21950600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:21949200-21950600	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr19:21949200-21950600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:21949200-21950600	Active TSS	Fetal Intestine Large	intestine
34	chr19:21949200-21950600	Active TSS	Fetal Stomach	stomach
35	chr19:21949200-21950600	Active TSS	NHDF-Ad	bronchial
36	chr19:21949200-21950600	Active TSS	NHEK	skin
37	chr19:21949200-21950600	Active TSS	Osteobl	bone
38	chr19:21949200-21950800	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr19:21949200-21950800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:21949200-21950800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:21949200-21950800	Active TSS	Primary T cells from cord blood	blood
42	chr19:21949200-21950800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:21949200-21950800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:21949200-21950800	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:21949200-21950800	Active TSS	Thymus	Thymus
46	chr19:21949200-21950800	Active TSS	K562	blood
47	chr19:21949200-21950800	Active TSS	NH-A	brain
48	chr19:21949200-21950800	Active TSS	NHLF	lung
49	chr19:21949400-21950400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr19:21949400-21950400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links