Variant report

Variant	rs66743282
Chromosome Location	chr19:41257952-41257953
allele	A/G
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	chr19:41255477-41257972	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF7	chr19:41256652-41257953	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:41255591-41257965	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:41255795-41257990	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:41255403-41257957	GM12891	blood:	n/a	n/a
6	YY1	chr19:41257537-41257984	GM12878	blood:	n/a	chr19:41257824-41257834
7	BCL3	chr19:41255259-41258065	A549	lung:	n/a	n/a
8	POLR2A	chr19:41255259-41257957	HL-60	blood:	n/a	n/a
9	POLR2A	chr19:41255536-41257993	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:41255295-41258005	U87	brain:	n/a	n/a
11	REST	chr19:41255871-41258036	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr19:41256564-41257957	K562	blood:	n/a	n/a
13	ZBTB33	chr19:41255684-41257975	A549	lung:	n/a	chr19:41257090-41257105 chr19:41257098-41257107
14	POLR2A	chr19:41255721-41258007	GM12878	blood:	n/a	n/a
15	TAF1	chr19:41255732-41257980	A549	lung:	n/a	n/a
16	POLR2A	chr19:41255185-41257990	GM12878	blood:	n/a	n/a
17	ATF2	chr19:41255823-41257952	GM12878	blood:	n/a	n/a
18	ESRRA	chr19:41255212-41258832	GM12878	blood:	n/a	chr19:41255368-41255382 chr19:41256561-41256571 chr19:41256561-41256571 chr19:41256557-41256573
19	RFX5	chr19:41255464-41258017	SK-N-SH	brain:	n/a	chr19:41256665-41256680 chr19:41256671-41256679 chr19:41256571-41256580 chr19:41256704-41256713
20	ATF3	chr19:41256068-41257967	A549	lung:	n/a	chr19:41256462-41256471
21	FOSL2	chr19:41255819-41257956	A549	lung:	n/a	chr19:41257024-41257033 chr19:41256703-41256712 chr19:41256665-41256674 chr19:41255893-41255905
22	BCLAF1	chr19:41255901-41257958	GM12878	blood:	n/a	n/a
23	SP1	chr19:41255694-41258003	A549	lung:	n/a	chr19:41256757-41256766 chr19:41256694-41256715 chr19:41256624-41256633 chr19:41257021-41257042 chr19:41256624-41256633 chr19:41256725-41256746 chr19:41256755-41256766 chr19:41256493-41256507 chr19:41256623-41256632 chr19:41256622-41256634 chr19:41256755-41256767 chr19:41256623-41256633 chr19:41256755-41256767
24	BCLAF1	chr19:41256700-41258024	GM12878	blood:	n/a	n/a
25	SIX5	chr19:41255261-41259082	A549	lung:	n/a	n/a
26	TCF12	chr19:41255907-41258007	A549	lung:	n/a	n/a
27	YY1	chr19:41257511-41258119	GM12878	blood:	n/a	chr19:41257824-41257834
28	EP300	chr19:41255684-41258029	A549	lung:	n/a	chr19:41257198-41257207 chr19:41255879-41255888 chr19:41256615-41256628
29	POLR2A	chr19:41255787-41258126	PFSK-1	brain:	n/a	n/a
30	REST	chr19:41255367-41257977	A549	lung:	n/a	n/a
31	TAF1	chr19:41255810-41257985	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:41257929-41257978	HUVEC	blood vessel:	n/a	n/a
33	TBL1XR1	chr19:41255790-41257996	GM12878	blood:	n/a	n/a
34	SP1	chr19:41255745-41257973	HCT-116	colon:	n/a	chr19:41256757-41256766 chr19:41256694-41256715 chr19:41256624-41256633 chr19:41257021-41257042 chr19:41256624-41256633 chr19:41256725-41256746 chr19:41256755-41256766 chr19:41256493-41256507 chr19:41256623-41256632 chr19:41256622-41256634 chr19:41256755-41256767 chr19:41256623-41256633 chr19:41256755-41256767
35	MYC	chr19:41255607-41258077	A549	lung:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
36	POLR2A	chr19:41255155-41258062	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:41255130-41259372	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr19:41256099-41258031	HepG2	liver:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
39	POLR2A	chr19:41255201-41258657	SK-N-MC	brain:	n/a	n/a
40	SIN3AK20	chr19:41255810-41258033	MCF-7	breast:	n/a	n/a
41	POLR2A	chr19:41255372-41257982	GM12891	blood:	n/a	n/a
42	CBX3	chr19:41255904-41257969	K562	blood:	n/a	n/a
43	MAX	chr19:41255678-41258047	A549	lung:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471
44	HEY1	chr19:41256634-41257999	HepG2	liver:	n/a	n/a
45	MXI1	chr19:41255610-41257970	IMR90	lung:	n/a	n/a
46	SP1	chr19:41255756-41257995	A549	lung:	n/a	chr19:41256757-41256766 chr19:41256694-41256715 chr19:41256624-41256633 chr19:41257021-41257042 chr19:41256624-41256633 chr19:41256725-41256746 chr19:41256755-41256766 chr19:41256493-41256507 chr19:41256623-41256632 chr19:41256622-41256634 chr19:41256755-41256767 chr19:41256623-41256633 chr19:41256755-41256767
47	POLR2A	chr19:41255516-41258007	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr19:41255654-41258055	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr19:41255253-41258081	GM12892	blood:	n/a	n/a
50	MAX	chr19:41255507-41258061	A549	lung:	n/a	chr19:41256419-41256432 chr19:41256421-41256430 chr19:41256420-41256430 chr19:41256416-41256435 chr19:41256461-41256472 chr19:41256420-41256431 chr19:41256419-41256432 chr19:41256422-41256431 chr19:41256460-41256473 chr19:41256417-41256432 chr19:41256461-41256470 chr19:41256421-41256430 chr19:41256462-41256471 chr19:41257268-41257276 chr19:41256461-41256472 chr19:41256419-41256432 chr19:41256462-41256471

No.	Distal block	Cell Line	Cell type
1	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
2	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
3	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
4	chr11:65190254..65190996-chr19:41257060..41258041,2	Hela-S3	cervix:
5	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
6	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
7	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
8	chr19:41253829..41256175-chr19:41256460..41259109,2	K562	blood:
9	chr19:41194676..41198444-chr19:41254531..41258137,9	MCF-7	breast:
10	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
11	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
12	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
13	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
14	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
15	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
16	chr19:41194241..41200533-chr19:41254244..41257966,10	K562	blood:
17	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:

Variant related genes	Relation type
SNRPA	TF binding region
C19orf54	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11668501	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12983335	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12984298	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4420642	1.00[ASN][1000 genomes]
rs55993576	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66599479	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66865752	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67083521	0.84[AFR][1000 genomes]
rs7249805	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253502	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7253804	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1793665	chr19:41249508-41258355	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
4	esv1803061	chr19:41249508-41258355	Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
5	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
6	esv1798663	chr19:41256519-41258355	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
7	esv1799699	chr19:41256519-41258355	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
8	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 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	chr19:41254600-41259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:41255400-41258200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:41255400-41258200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:41255400-41258600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:41255400-41258600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:41255600-41258000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr19:41255600-41258200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:41255600-41258600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:41255600-41258800	Active TSS	Gastric	stomach
10	chr19:41255600-41259000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr19:41255800-41258400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:41255800-41258400	Active TSS	Fetal Kidney	kidney
13	chr19:41255800-41258600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:41255800-41258600	Active TSS	Esophagus	oesophagus
15	chr19:41255800-41258600	Active TSS	GM12878-XiMat	blood
16	chr19:41255800-41258800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:41255800-41258800	Active TSS	Right Ventricle	heart
18	chr19:41255800-41259000	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr19:41256000-41258000	Active TSS	Aorta	Aorta
20	chr19:41256000-41258000	Active TSS	Left Ventricle	heart
21	chr19:41256000-41258000	Active TSS	Spleen	Spleen
22	chr19:41256000-41258200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:41256000-41258200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:41256000-41258200	Active TSS	Liver	Liver
25	chr19:41256000-41258200	Active TSS	Lung	lung
26	chr19:41256000-41258200	Active TSS	Psoas Muscle	Psoas
27	chr19:41256000-41258400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:41256000-41258400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:41256000-41258400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:41256000-41258600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:41256000-41258600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:41256000-41258600	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr19:41256000-41258600	Active TSS	Ovary	ovary
34	chr19:41256000-41258600	Active TSS	Pancreas	Pancrea
35	chr19:41256000-41258600	Active TSS	HSMM	muscle
36	chr19:41256000-41258800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:41256000-41258800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr19:41256200-41258000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:41256200-41258000	Active TSS	Fetal Stomach	stomach
40	chr19:41256200-41258200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:41256200-41258200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:41256200-41258200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:41256200-41258200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:41256200-41258200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:41256200-41258200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:41256200-41258200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:41256200-41258200	Active TSS	Brain Angular Gyrus	brain
48	chr19:41256200-41258200	Active TSS	Brain Anterior Caudate	brain
49	chr19:41256200-41258200	Active TSS	Brain Hippocampus Middle	brain
50	chr19:41256200-41258200	Active TSS	Colonic Mucosa	Colon

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