Variant report

Variant	rs310471
Chromosome Location	chr19:56158720-56158721
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56158426-56160162	K562	blood:	n/a	n/a
2	POLR2A	chr19:56158684-56159850	HEK293	kidney:	n/a	n/a
3	PAX5	chr19:56158677-56158993	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:56158689-56159025	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr19:56158652-56159538	ECC-1	luminal epithelium:	n/a	n/a
6	RCOR1	chr19:56158679-56160151	K562	blood:	n/a	n/a
7	POLR2A	chr19:56158473-56159119	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:56158561-56158754	H1-hESC	embryonic stem cell:	n/a	n/a
9	RUNX3	chr19:56158619-56160103	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:56158624-56160441	GM12878	blood:	n/a	n/a
11	RELA	chr19:56158525-56160062	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:56157862-56160141	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:56158674-56160309	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr19:56158648-56159541	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:56158338-56160522	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:56158168-56160639	HepG2	liver:	n/a	n/a
17	KAP1	chr19:56158475-56159593	U2OS	brain:	n/a	n/a
18	POLR2A	chr19:56158375-56159704	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr19:56158096-56160099	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr19:56158219-56160915	PANC-1	pancreas:	n/a	n/a
21	RELA	chr19:56158468-56159552	GM10847	blood:	n/a	n/a
22	MTA3	chr19:56158476-56161118	GM12878	blood:	n/a	n/a
23	MTA3	chr19:56158453-56160712	GM12878	blood:	n/a	n/a
24	EP300	chr19:56158699-56159764	ECC-1	luminal epithelium:	n/a	chr19:56159605-56159614 chr19:56159602-56159611
25	NFIC	chr19:56158688-56159101	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:56158616-56159464	U87	brain:	n/a	n/a
27	POLR2A	chr19:56158451-56160173	GM18505	blood:	n/a	n/a
28	POLR2A	chr19:56158691-56159195	GM12891	blood:	n/a	n/a
29	POLR2A	chr19:56158591-56159870	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr19:56158346-56159568	GM12892	blood:	n/a	n/a
31	RUNX3	chr19:56158523-56160075	GM12878	blood:	n/a	n/a
32	TCF12	chr19:56158549-56159657	ECC-1	luminal epithelium:	n/a	chr19:56159516-56159526
33	POLR2A	chr19:56158462-56159390	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:56158336-56160689	K562	blood:	n/a	n/a
35	SP1	chr19:56158639-56159867	A549	lung:	n/a	chr19:56159336-56159350 chr19:56159844-56159858 chr19:56159340-56159349 chr19:56159339-56159350
36	GATA3	chr19:56158707-56160200	A549	lung:	n/a	n/a
37	ZNF263	chr19:56158489-56159585	HEK293-T-REx	kidney:	n/a	n/a
38	POLR2A	chr19:56158330-56160505	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:56158064-56159360	MCF10A-Er-Src	breast:	n/a	n/a
40	PML	chr19:56158525-56160361	GM12878	blood:	n/a	n/a
41	RELA	chr19:56158523-56160016	GM18951	blood:	n/a	n/a
42	POLR2A	chr19:56158712-56159003	GM12891	blood:	n/a	n/a
43	POLR2A	chr19:56158173-56160679	GM12891	blood:	n/a	n/a
44	BCLAF1	chr19:56158657-56159605	GM12878	blood:	n/a	chr19:56159585-56159598
45	MAZ	chr19:56158475-56160363	IMR90	lung:	n/a	chr19:56159340-56159350 chr19:56159809-56159818 chr19:56159876-56159885 chr19:56159689-56159699 chr19:56159764-56159774
46	POLR2A	chr19:56158403-56160094	GM18951	blood:	n/a	n/a
47	POLR2A	chr19:56158704-56161230	GM19193	blood:	n/a	n/a
48	POLR2A	chr19:56158176-56161389	K562	blood:	n/a	n/a
49	POLR2A	chr19:56158015-56160377	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr19:56158339-56159575	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56158714-56158764	AG10803	skin:	n/a
2	chr19:56158714-56158764	MCF10A-Er-Src	breast:	n/a
3	chr19:56158714-56158764	GM06990	blood:	n/a
4	chr19:56158714-56158764	GM12892	blood:	n/a
5	chr19:56158714-56158764	SKMC	muscle:	n/a
6	chr19:56158714-56158764	K562	blood:	n/a
7	chr19:56158714-56158764	AG04450	lung:	fetal
8	chr19:56158714-56158764	LNCaP	prostate:	n/a
9	chr19:56158714-56158764	HNPCEpiC	eye:	n/a
10	chr19:56158714-56158764	CMK	blood:	n/a
11	chr19:56158714-56158764	SAEC	small airway:	n/a
12	chr19:56158714-56158764	HEEpiC	esophagus:	n/a
13	chr19:56158714-56158764	ovcar-3	ovarian:	n/a
14	chr19:56158714-56158764	MCF-7	breast:	n/a
15	chr19:56158714-56158764	Hela-S3	cervix:	n/a
16	chr19:56158714-56158764	PANC-1	pancreas:	n/a
17	chr19:56158714-56158764	RPTEC	kidney:	n/a
18	chr19:56158714-56158764	U87	brain:	n/a
19	chr19:56158714-56158764	NB4	blood:	n/a
20	chr19:56158714-56158764	NT2-D1	testis:	n/a
21	chr19:56158714-56158764	Hepatocyte	liver:	n/a
22	chr19:56158714-56158764	H1-hESC	embryonic stem cell:	embryo
23	chr19:56158714-56158764	GM12878	blood:	n/a
24	chr19:56158714-56158764	BJ	skin:	n/a
25	chr19:56158714-56158764	HCF	heart:	n/a
26	chr19:56158714-56158764	HMEC	breast:	n/a
27	chr19:56158714-56158764	HRPEpiC	eye:	n/a
28	chr19:56158714-56158764	SK-N-SH	brain:	n/a
29	chr19:56158714-56158764	ProgFib	skin:	n/a
30	chr19:56158714-56158764	NHDF-neo	bronchial:	n/a
31	chr19:56158714-56158764	NHBE	bronchial:	n/a
32	chr19:56158714-56158764	AG09319	gingival:	n/a
33	chr19:56158714-56158764	HCM	heart:	n/a
34	chr19:56158714-56158764	HUVEC	blood vessel:	n/a
35	chr19:56158714-56158764	HPAEpiC	pulmonary alveolar:	n/a
36	chr19:56158714-56158764	HEK293	kidney:	embryo
37	chr19:56158714-56158764	SK-N-SH_RA	brain:	n/a
38	chr19:56158714-56158764	HCPEpiC	choroid plexus:	n/a
39	chr19:56158714-56158764	IMR90	lung:	fetal
40	chr19:56158714-56158764	AG04449	skin:	fetal
41	chr19:56158714-56158764	Jurkat	blood:	n/a
42	chr19:56158714-56158764	NH-A	brain:	n/a
43	chr19:56158714-56158764	PFSK-1	brain:	n/a
44	chr19:56158714-56158764	GM19239	blood:	n/a
45	chr19:56158714-56158764	HAEpiC	amniotic membrane:	n/a
46	chr19:56158714-56158764	PrEC	prostate:	n/a
47	chr19:56158714-56158764	HepG2	liver:	n/a
48	chr19:56158714-56158764	HIPEpiC	eye:	n/a
49	chr19:56158714-56158764	AoSMC	blood vessel:	n/a
50	chr19:56158714-56158764	GM12891	blood:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55951636..55954321-chr19:56156627..56158922,2	K562	blood:
2	chr19:56158129..56161096-chr19:56185326..56187791,3	MCF-7	breast:
3	chr19:55915993..55918955-chr19:56157443..56159330,2	K562	blood:

No data

Variant related genes	Relation type
CCDC106	TF binding region
CCDC106	CpG island
ENSG00000267523	Chromatin interaction
ENSG00000187902	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11545669	1.00[AFR][1000 genomes]
rs310439	1.00[AFR][1000 genomes]
rs310443	1.00[AFR][1000 genomes]
rs310470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310474	1.00[EUR][1000 genomes]
rs507498	0.83[EUR][1000 genomes]
rs520125	0.83[ASN][1000 genomes]
rs522669	0.83[ASN][1000 genomes]
rs553947	1.00[ASN][1000 genomes]
rs56038728	1.00[AFR][1000 genomes]
rs57063593	0.83[EUR][1000 genomes]
rs581023	0.84[EUR][1000 genomes]
rs600106	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs612211	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630491	1.00[AFR][1000 genomes]
rs636466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637788	0.89[EUR][1000 genomes]
rs644230	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679577	0.83[EUR][1000 genomes]
rs680444	0.83[EUR][1000 genomes]
rs681433	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7246799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251872	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889091	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 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	chr19:56155800-56158800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:56156000-56158800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:56156200-56158800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:56156200-56158800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:56156200-56158800	Weak transcription	Right Atrium	heart
6	chr19:56156400-56158800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:56156600-56158800	Weak transcription	Colonic Mucosa	Colon
8	chr19:56157000-56159000	Weak transcription	Gastric	stomach
9	chr19:56157000-56159000	Weak transcription	Ovary	ovary
10	chr19:56157000-56159200	Weak transcription	Aorta	Aorta
11	chr19:56157200-56158800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:56157200-56158800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:56157200-56158800	Weak transcription	Lung	lung
14	chr19:56157200-56158800	Weak transcription	HSMM	muscle
15	chr19:56157200-56159000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:56157400-56158800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:56157400-56158800	Weak transcription	HMEC	breast
18	chr19:56157400-56158800	Weak transcription	NHEK	skin
19	chr19:56157800-56158800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:56158200-56158800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr19:56158200-56158800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:56158200-56158800	Enhancers	Liver	Liver
23	chr19:56158200-56158800	Enhancers	Thymus	Thymus
24	chr19:56158200-56160800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:56158200-56161800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:56158400-56158800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
27	chr19:56158400-56158800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:56158400-56158800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:56158400-56158800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:56158400-56158800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr19:56158400-56158800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr19:56158400-56158800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:56158400-56158800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:56158400-56158800	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:56158400-56158800	Enhancers	Duodenum Mucosa	Duodenum
36	chr19:56158400-56158800	Enhancers	Esophagus	oesophagus
37	chr19:56158400-56158800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr19:56158400-56158800	Genic enhancers	Fetal Intestine Small	intestine
39	chr19:56158400-56158800	Genic enhancers	Fetal Stomach	stomach
40	chr19:56158400-56158800	Enhancers	Fetal Thymus	thymus
41	chr19:56158400-56158800	Enhancers	HSMMtube	muscle
42	chr19:56158400-56158800	Transcr. at gene 5' and 3'	K562	blood
43	chr19:56158400-56158800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr19:56158400-56158800	Enhancers	NHLF	lung
45	chr19:56158400-56159000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr19:56158400-56159000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr19:56158400-56159000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:56158400-56159000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr19:56158400-56159000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:56158400-56159000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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