Variant report

Variant	rs3843754
Chromosome Location	chr19:38807184-38807185
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	NR2F2	chr19:38805776-38807445	K562	blood:	n/a	chr19:38806412-38806427 chr19:38806409-38806424
2	STAT5A	chr19:38806701-38807288	GM12878	blood:	n/a	n/a
3	HEY1	chr19:38806681-38807288	K562	blood:	n/a	n/a
4	SIN3AK20	chr19:38806703-38807356	A549	lung:	n/a	n/a
5	GTF3C2	chr19:38806271-38807387	K562	blood:	n/a	n/a
6	POU2F2	chr19:38806698-38807284	GM12891	blood:	n/a	n/a
7	BCL3	chr19:38805728-38807472	A549	lung:	n/a	n/a
8	FOXA1	chr19:38806986-38807199	T-47D	breast:	n/a	n/a
9	ZMIZ1	chr19:38805988-38807224	K562	blood:	n/a	n/a
10	REST	chr19:38806574-38807305	A549	lung:	n/a	n/a
11	CBX3	chr19:38806405-38807275	K562	blood:	n/a	n/a
12	ZNF384	chr19:38806767-38807233	GM12878	blood:	n/a	n/a
13	E2F6	chr19:38806052-38807221	A549	lung:	n/a	chr19:38806619-38806628 chr19:38807144-38807161
14	ARID3A	chr19:38806755-38807222	K562	blood:	n/a	n/a
15	SIX5	chr19:38806935-38807305	GM12878	blood:	n/a	chr19:38807166-38807180
16	RCOR1	chr19:38807014-38807207	HepG2	liver:	n/a	n/a
17	ZNF143	chr19:38806887-38807283	Hela-S3	cervix:	n/a	chr19:38807160-38807178
18	KAP1	chr19:38806762-38807185	U2OS	brain:	n/a	n/a
19	POLR2A	chr19:38806017-38808215	K562	blood:	n/a	n/a
20	MAZ	chr19:38806184-38807288	GM12878	blood:	n/a	n/a
21	ZNF384	chr19:38805813-38807254	K562	blood:	n/a	n/a
22	IRF1	chr19:38805932-38807308	K562	blood:	n/a	chr19:38806740-38806754 chr19:38807245-38807259 chr19:38806636-38806645 chr19:38807249-38807259
23	MAFF	chr19:38807006-38807311	K562	blood:	n/a	n/a
24	SP1	chr19:38805824-38807302	A549	lung:	n/a	chr19:38806671-38806681 chr19:38806670-38806682 chr19:38806665-38806679 chr19:38806672-38806681 chr19:38806635-38806656 chr19:38806670-38806682 chr19:38806613-38806623
25	PML	chr19:38806602-38807217	GM12878	blood:	n/a	n/a
26	FOXA1	chr19:38806970-38807294	HepG2	liver:	n/a	n/a
27	RCOR1	chr19:38806029-38808321	K562	blood:	n/a	n/a
28	SIN3AK20	chr19:38806724-38807213	A549	lung:	n/a	n/a
29	GTF3C2	chr19:38806854-38807351	Hela-S3	cervix:	n/a	n/a
30	ZBTB33	chr19:38806875-38807356	A549	lung:	n/a	n/a
31	USF2	chr19:38806822-38807211	Hela-S3	cervix:	n/a	n/a
32	TBL1XR1	chr19:38805898-38808243	K562	blood:	n/a	n/a
33	FOXA2	chr19:38806830-38807368	A549	lung:	n/a	n/a
34	JUND	chr19:38806043-38808215	K562	blood:	n/a	n/a
35	JUN	chr19:38805648-38808373	K562	blood:	n/a	n/a
36	PML	chr19:38806677-38807305	K562	blood:	n/a	n/a
37	CEBPB	chr19:38806448-38807336	A549	lung:	n/a	n/a
38	ZNF143	chr19:38806354-38807356	GM12878	blood:	n/a	chr19:38806482-38806492 chr19:38807160-38807178 chr19:38806671-38806689
39	SMC3	chr19:38806213-38807219	Hela-S3	cervix:	n/a	n/a
40	SP1	chr19:38805858-38807353	A549	lung:	n/a	chr19:38806671-38806681 chr19:38806670-38806682 chr19:38806665-38806679 chr19:38806672-38806681 chr19:38806635-38806656 chr19:38806670-38806682 chr19:38806613-38806623
41	PBX3	chr19:38806163-38807322	A549	lung:	n/a	chr19:38806791-38806800
42	POU2F2	chr19:38806338-38807397	GM12878	blood:	n/a	chr19:38806669-38806681 chr19:38806671-38806683 chr19:38806680-38806692
43	CHD2	chr19:38806083-38807303	GM12878	blood:	n/a	chr19:38806664-38806674
44	MAZ	chr19:38806026-38807215	K562	blood:	n/a	n/a
45	ETS1	chr19:38806168-38807353	A549	lung:	n/a	chr19:38806562-38806573 chr19:38807167-38807180 chr19:38807284-38807291
46	SIX5	chr19:38806389-38807352	A549	lung:	n/a	chr19:38807166-38807180
47	POLR2A	chr19:38805864-38808241	K562	blood:	n/a	n/a
48	IRF1	chr19:38805903-38807375	K562	blood:	n/a	chr19:38806740-38806754 chr19:38807245-38807259 chr19:38806636-38806645 chr19:38807249-38807259
49	POLR2A	chr19:38806236-38807216	PANC-1	pancreas:	n/a	n/a
50	POU2F2	chr19:38806755-38807341	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38804679..38808674-chr19:38824887..38827856,7	K562	blood:
2	chr19:38805296..38807779-chr19:38877097..38880049,2	K562	blood:
3	chr19:38806332..38809400-chr19:38825014..38828541,5	K562	blood:
4	chr19:38800007..38802686-chr19:38805252..38808238,5	K562	blood:
5	chr19:38746183..38748575-chr19:38806704..38809483,2	K562	blood:
6	chr19:38804471..38807313-chr19:38874109..38876554,2	MCF-7	breast:
7	chr19:38805271..38808237-chr19:39322535..39325453,2	K562	blood:
8	chr19:38753883..38755727-chr19:38805197..38807267,2	MCF-7	breast:
9	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:
10	chr19:38806279..38807928-chr19:38863720..38866328,2	K562	blood:
11	chr19:38745470..38748025-chr19:38806544..38809528,4	K562	blood:

Variant related genes	Relation type
KCNK6	TF binding region
YIF1B	TF binding region
ENSG00000179168	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11666449	0.86[YRI][hapmap]
rs11881305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12609247	0.93[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12611255	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1821284	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2270095	1.00[ASW][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2286475	0.93[GIH][hapmap];0.95[TSI][hapmap]
rs2286476	0.81[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap]
rs2304176	0.96[GIH][hapmap];0.97[TSI][hapmap]
rs3178327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35436012	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4312417	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4802324	0.86[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803999	0.83[EUR][1000 genomes]
rs59898212	0.81[AFR][1000 genomes]
rs61160177	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71354995	0.94[EUR][1000 genomes]
rs7252835	0.86[AFR][1000 genomes]
rs7253960	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7257537	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260137	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73043010	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8112211	1.00[GIH][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap]

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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3843754	C19orf33	cis	Nerve Tibial	GTEx
rs3843754	C19orf33	cis	normal skin	skin_eQTL
rs3843754	SELV	cis	parietal	SCAN
rs3843754	C19orf33	cis	uninvolved skin	skin_eQTL
rs3843754	APOC4	cis	cerebellum	SCAN
rs3843754	C19orf33	cis	lesional skin	skin_eQTL
rs3843754	PSG4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38805400-38807200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:38805400-38807400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:38805400-38807400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:38805400-38807400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:38805600-38807200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:38805600-38807400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:38805600-38807400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:38805800-38807200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:38805800-38807200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:38805800-38807200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr19:38805800-38807200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:38805800-38807200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:38805800-38807200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:38805800-38807200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:38805800-38807200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr19:38805800-38807200	Active TSS	Psoas Muscle	Psoas
17	chr19:38805800-38807200	Active TSS	Right Ventricle	heart
18	chr19:38805800-38807200	Active TSS	NHLF	lung
19	chr19:38805800-38807400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:38805800-38807400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr19:38805800-38807400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr19:38805800-38807400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr19:38805800-38807400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:38805800-38807400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38805800-38807400	Active TSS	Brain Angular Gyrus	brain
26	chr19:38805800-38807400	Active TSS	Brain Germinal Matrix	brain
27	chr19:38806000-38807200	Active TSS	Fetal Kidney	kidney
28	chr19:38806000-38807400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:38806000-38807400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:38806200-38807200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr19:38806200-38807200	Active TSS	Aorta	Aorta
32	chr19:38806200-38807200	Active TSS	Brain Substantia Nigra	brain
33	chr19:38806200-38807200	Active TSS	Left Ventricle	heart
34	chr19:38806200-38807200	Active TSS	Ovary	ovary
35	chr19:38806200-38807200	Active TSS	Pancreas	Pancrea
36	chr19:38806200-38807200	Active TSS	Placenta Amnion	Placenta Amnion
37	chr19:38806200-38807200	Active TSS	Thymus	Thymus
38	chr19:38806200-38807200	Active TSS	GM12878-XiMat	blood
39	chr19:38806200-38807200	Bivalent/Poised TSS	HepG2	liver
40	chr19:38806200-38807400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:38806200-38807400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:38806200-38807400	Active TSS	A549	lung
43	chr19:38806200-38807400	Active TSS	Hela-S3	cervix
44	chr19:38806200-38807800	Active TSS	Brain Anterior Caudate	brain
45	chr19:38806200-38807800	Active TSS	Brain Cingulate Gyrus	brain
46	chr19:38806200-38808000	Active TSS	Brain Hippocampus Middle	brain
47	chr19:38806400-38807200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr19:38806400-38807200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:38806400-38807200	Active TSS	Fetal Intestine Large	intestine
50	chr19:38806400-38807200	Active TSS	Skeletal Muscle Female	skeletal muscle

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