Variant report

Variant	rs1123301
Chromosome Location	chr19:40023308-40023309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:292)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:292 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40023181-40023623	A549	lung:	n/a	n/a
2	MAX	chr19:40023143-40023655	K562	blood:	n/a	n/a
3	TCF12	chr19:40023039-40023857	ECC-1	luminal epithelium:	n/a	n/a
4	SMC3	chr19:40023178-40023790	GM12878	blood:	n/a	n/a
5	SP4	chr19:40022992-40023797	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:40022810-40023728	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:40023298-40023628	K562	blood:	n/a	n/a
8	RXRA	chr19:40023301-40023699	GM12878	blood:	n/a	n/a
9	PML	chr19:40022746-40023873	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:40023176-40023639	A549	lung:	n/a	n/a
11	TAF1	chr19:40023287-40023657	K562	blood:	n/a	n/a
12	RFX5	chr19:40022964-40023763	Hela-S3	cervix:	n/a	n/a
13	RELA	chr19:40023232-40023760	GM19099	blood:	n/a	n/a
14	GTF2F1	chr19:40023272-40023694	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr19:40022910-40023764	K562	blood:	n/a	n/a
16	RCOR1	chr19:40023050-40023720	HepG2	liver:	n/a	n/a
17	YY1	chr19:40023090-40023662	SK-N-SH_RA	brain:	n/a	n/a
18	TFAP2C	chr19:40022773-40023818	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr19:40023141-40023782	HepG2	liver:	n/a	n/a
20	PAX5	chr19:40023181-40023793	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:40022884-40023640	K562	blood:	n/a	n/a
22	YY1	chr19:40023047-40023737	ECC-1	luminal epithelium:	n/a	n/a
23	MYC	chr19:40023286-40023696	MCF-7	breast:	n/a	n/a
24	POLR2A	chr19:40023162-40023638	U87	brain:	n/a	n/a
25	ZBTB33	chr19:40023013-40023782	A549	lung:	n/a	n/a
26	POLR2A	chr19:40023238-40023657	GM12878	blood:	n/a	n/a
27	CTCF	chr19:40022001-40025161	A549	lung:	n/a	n/a
28	MTA3	chr19:40022726-40023770	GM12878	blood:	n/a	n/a
29	RAD21	chr19:40022753-40024037	A549	lung:	n/a	n/a
30	PML	chr19:40023025-40023719	K562	blood:	n/a	n/a
31	EP300	chr19:40023269-40023685	GM12878	blood:	n/a	n/a
32	RAD21	chr19:40023244-40023914	A549	lung:	n/a	n/a
33	BCLAF1	chr19:40023073-40023819	GM12878	blood:	n/a	n/a
34	MXI1	chr19:40023228-40023688	K562	blood:	n/a	n/a
35	E2F6	chr19:40022605-40023802	A549	lung:	n/a	chr19:40023502-40023511 chr19:40023553-40023562
36	ELK1	chr19:40023289-40023691	Hela-S3	cervix:	n/a	n/a
37	ZNF263	chr19:40022541-40023853	HEK293-T-REx	kidney:	n/a	n/a
38	YY1	chr19:40023067-40023680	HepG2	liver:	n/a	n/a
39	RAD21	chr19:40023298-40023807	HepG2	liver:	n/a	n/a
40	POLR2A	chr19:40023095-40023745	GM18951	blood:	n/a	n/a
41	POLR2A	chr19:40023235-40023707	HUVEC	blood vessel:	n/a	n/a
42	YY1	chr19:40023287-40023661	HCT-116	colon:	n/a	n/a
43	ATF2	chr19:40023131-40023850	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:40023145-40023684	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr19:40023208-40023704	MCF-7	breast:	n/a	n/a
46	TBP	chr19:40023194-40023680	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr19:40022981-40023704	H1-hESC	embryonic stem cell:	n/a	n/a
48	UBTF	chr19:40022973-40023484	K562	blood:	n/a	n/a
49	POLR2A	chr19:40023259-40023625	HepG2	liver:	n/a	n/a
50	ATF3	chr19:40022437-40023864	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40023281-40023331	IMR90	lung:	fetal
2	chr19:40023281-40023331	U87	brain:	n/a
3	chr19:40023281-40023331	Hela-S3	cervix:	n/a
4	chr19:40023281-40023331	ECC-1	luminal epithelium:	n/a
5	chr19:40023281-40023331	Jurkat	blood:	n/a
6	chr19:40023281-40023331	HUVEC	blood vessel:	n/a
7	chr19:40023281-40023331	HCPEpiC	choroid plexus:	n/a
8	chr19:40023281-40023331	MCF-7	breast:	n/a
9	chr19:40023281-40023331	H1-hESC	embryonic stem cell:	embryo
10	chr19:40023281-40023331	AG09319	gingival:	n/a
11	chr19:40023281-40023331	HL-60	blood:	n/a
12	chr19:40023281-40023331	K562	blood:	n/a
13	chr19:40023281-40023331	PANC-1	pancreas:	n/a
14	chr19:40023281-40023331	GM06990	blood:	n/a
15	chr19:40023281-40023331	NH-A	brain:	n/a
16	chr19:40023281-40023331	AoSMC	blood vessel:	n/a
17	chr19:40023281-40023331	HNPCEpiC	eye:	n/a
18	chr19:40023281-40023331	HRPEpiC	eye:	n/a
19	chr19:40023281-40023331	HIPEpiC	eye:	n/a
20	chr19:40023281-40023331	Hepatocyte	liver:	n/a
21	chr19:40023281-40023331	HPAEpiC	pulmonary alveolar:	n/a
22	chr19:40023281-40023331	HRE	kidney:	n/a
23	chr19:40023281-40023331	BE2_C	brain:	n/a
24	chr19:40023281-40023331	NHDF-neo	bronchial:	n/a
25	chr19:40023281-40023331	AG09309	skin:	n/a
26	chr19:40023281-40023331	HEK293	kidney:	embryo
27	chr19:40023281-40023331	PrEC	prostate:	n/a
28	chr19:40023281-40023331	LNCaP	prostate:	n/a
29	chr19:40023281-40023331	AG10803	skin:	n/a
30	chr19:40023281-40023331	HCF	heart:	n/a
31	chr19:40023281-40023331	HAEpiC	amniotic membrane:	n/a
32	chr19:40023281-40023331	HRCEpiC	kidney:	n/a
33	chr19:40023281-40023331	ovcar-3	ovarian:	n/a
34	chr19:40023281-40023331	Caco-2	colon:	n/a
35	chr19:40023281-40023331	AG04449	skin:	fetal
36	chr19:40023281-40023331	MCF10A-Er-Src	breast:	n/a
37	chr19:40023281-40023331	SK-N-SH	brain:	n/a
38	chr19:40023281-40023331	HMEC	breast:	n/a
39	chr19:40023281-40023331	NB4	blood:	n/a
40	chr19:40023281-40023331	AG04450	lung:	fetal
41	chr19:40023281-40023331	HepG2	liver:	n/a
42	chr19:40023281-40023331	SKMC	muscle:	n/a
43	chr19:40023281-40023331	BJ	skin:	n/a
44	chr19:40023281-40023331	HCT-116	colon:	n/a
45	chr19:40023281-40023331	GM12878	blood:	n/a
46	chr19:40023281-40023331	HCM	heart:	n/a
47	chr19:40023281-40023331	GM19239	blood:	n/a
48	chr19:40023281-40023331	NT2-D1	testis:	n/a
49	chr19:40023281-40023331	SK-N-SH_RA	brain:	n/a
50	chr19:40023281-40023331	T-47D	breast:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39934791..39938517-chr19:40022234..40026334,4	K562	blood:
2	chr19:39969179..39972823-chr19:40019268..40024259,8	K562	blood:
3	chr19:39898615..39903463-chr19:40021264..40024360,6	K562	blood:
4	chr19:39963222..39966724-chr19:40022598..40024872,4	K562	blood:
5	chr19:40023014..40023615-chr5:65439737..65440573,2	Hela-S3	cervix:
6	chr19:39935867..39937651-chr19:40022035..40024212,2	MCF-7	breast:
7	chr19:39902534..39904778-chr19:40022453..40024067,3	MCF-7	breast:
8	chr19:39934545..39937545-chr19:40023023..40025430,4	MCF-7	breast:
9	chr19:39880509..39882503-chr19:40021734..40025038,3	K562	blood:
10	chr19:39832237..39832969-chr19:40023143..40024117,2	K562	blood:
11	chr19:39961748..39964722-chr19:40022955..40025016,3	K562	blood:
12	chr19:40021563..40023552-chr19:40334495..40337354,2	K562	blood:
13	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
14	chr19:39925075..39926642-chr19:40022135..40025107,3	K562	blood:
15	chr19:39969762..39972823-chr19:40020818..40024781,5	K562	blood:
16	chr19:39988746..39992361-chr19:40020493..40024366,5	MCF-7	breast:
17	chr19:39898615..39904728-chr19:40019936..40025504,8	K562	blood:
18	chr19:40019907..40024445-chr19:40029285..40031709,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SELV.1-2	chr19:40023052-40023488	ENSG00000269792.1

No data

Variant related genes	Relation type
TDGF1P7	TF binding region
TDGF1P7	CpG island
ENSG00000105197	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000105193	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10439100	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12608613	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1368468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803255	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6508867	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508868	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7245901	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7246072	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8108097	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8110685	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911694	chr19:40015907-40031369	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv137930	chr19:40019489-40027856	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr19:40021800-40024000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:40021800-40024000	Active TSS	Hela-S3	cervix
3	chr19:40022000-40023800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:40022200-40023600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:40022200-40023600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:40022200-40023600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:40022200-40023600	Active TSS	K562	blood
8	chr19:40022200-40023600	Active TSS	NHDF-Ad	bronchial
9	chr19:40022200-40023800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr19:40022200-40023800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:40022200-40023800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:40022200-40023800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:40022400-40023600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr19:40022400-40023600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr19:40022400-40023600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr19:40022400-40023600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:40022400-40023600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr19:40022400-40023600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:40022400-40023600	Active TSS	Brain Substantia Nigra	brain
20	chr19:40022400-40023600	Active TSS	Fetal Intestine Small	intestine
21	chr19:40022400-40023600	Active TSS	Ovary	ovary
22	chr19:40022400-40023600	Active TSS	GM12878-XiMat	blood
23	chr19:40022400-40023600	Active TSS	HSMM	muscle
24	chr19:40022400-40023600	Active TSS	HSMMtube	muscle
25	chr19:40022400-40023800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:40022400-40023800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:40022400-40023800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:40022400-40023800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:40022400-40023800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:40022400-40023800	Active TSS	Right Atrium	heart
31	chr19:40022400-40023800	Active TSS	Right Ventricle	heart
32	chr19:40022600-40023400	Bivalent/Poised TSS	HepG2	liver
33	chr19:40022600-40023600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr19:40022600-40023600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:40022600-40023600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:40022600-40023600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:40022600-40023600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:40022600-40023600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:40022600-40023600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:40022600-40023600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:40022600-40023600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:40022600-40023600	Active TSS	Aorta	Aorta
43	chr19:40022600-40023600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr19:40022600-40023600	Active TSS	NH-A	brain
45	chr19:40022600-40023600	Active TSS	NHLF	lung
46	chr19:40022600-40023800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:40022600-40023800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:40022600-40023800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:40022600-40023800	Active TSS	Fetal Kidney	kidney
50	chr19:40022600-40023800	Flanking Active TSS	Fetal Muscle Trunk	muscle

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