Variant report

Variant	rs11667774
Chromosome Location	chr19:40854454-40854455
allele	C/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	TBL1XR1	chr19:40854068-40854858	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:40854021-40854828	GM18526	blood:	n/a	n/a
3	CHD2	chr19:40854263-40854666	K562	blood:	n/a	chr19:40854317-40854327 chr19:40854299-40854309 chr19:40854536-40854543
4	IRF1	chr19:40853820-40855040	K562	blood:	n/a	n/a
5	BHLHE40	chr19:40853924-40854735	K562	blood:	n/a	n/a
6	MAX	chr19:40853935-40854907	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:40854398-40854862	U87	brain:	n/a	n/a
8	HA-E2F1	chr19:40853846-40854731	MCF-7	breast:	n/a	chr19:40854581-40854590 chr19:40854553-40854562 chr19:40854690-40854699 chr19:40854536-40854543
9	POLR2A	chr19:40853832-40855318	K562	blood:	n/a	n/a
10	POLR2A	chr19:40854045-40854867	HEK293	kidney:	n/a	n/a
11	ATF3	chr19:40854131-40854758	HepG2	liver:	n/a	chr19:40854243-40854252 chr19:40854520-40854529 chr19:40854319-40854328 chr19:40854692-40854701
12	USF1	chr19:40853761-40855378	A549	lung:	n/a	chr19:40854419-40854430
13	TEAD4	chr19:40853795-40855021	K562	blood:	n/a	n/a
14	TCF12	chr19:40854358-40854572	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:40854074-40854825	HCT-116	colon:	n/a	n/a
16	IRF1	chr19:40854093-40855178	K562	blood:	n/a	n/a
17	CHD2	chr19:40854191-40854587	H1-hESC	embryonic stem cell:	n/a	chr19:40854317-40854327 chr19:40854299-40854309 chr19:40854536-40854543
18	BHLHE40	chr19:40854179-40854669	GM12878	blood:	n/a	n/a
19	GABPA	chr19:40853946-40854572	K562	blood:	n/a	chr19:40854258-40854267 chr19:40854214-40854223
20	ATF3	chr19:40854240-40854648	K562	blood:	n/a	chr19:40854243-40854252 chr19:40854520-40854529 chr19:40854319-40854328
21	TCF12	chr19:40853672-40855441	A549	lung:	n/a	n/a
22	MAX	chr19:40854089-40854874	SK-N-SH	brain:	n/a	n/a
23	FOSL2	chr19:40854209-40854631	A549	lung:	n/a	chr19:40854527-40854536 chr19:40854259-40854268
24	POLR2A	chr19:40853848-40854974	Hela-S3	cervix:	n/a	n/a
25	USF2	chr19:40854177-40854750	GM12878	blood:	n/a	chr19:40854464-40854475 chr19:40854419-40854430
26	POLR2A	chr19:40853992-40854916	Gliobla	brain:	n/a	n/a
27	POLR2A	chr19:40854042-40854850	GM12892	blood:	n/a	n/a
28	ETS1	chr19:40854130-40854606	A549	lung:	n/a	chr19:40854299-40854310 chr19:40854258-40854269 chr19:40854314-40854327
29	POLR2A	chr19:40853983-40854933	PFSK-1	brain:	n/a	n/a
30	ELK1	chr19:40854200-40854623	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:40853978-40854784	A549	lung:	n/a	n/a
32	TAF1	chr19:40854113-40854840	ECC-1	luminal epithelium:	n/a	n/a
33	NFIC	chr19:40854109-40854842	GM12878	blood:	n/a	n/a
34	ATF3	chr19:40854100-40854753	A549	lung:	n/a	chr19:40854243-40854252 chr19:40854520-40854529 chr19:40854319-40854328 chr19:40854692-40854701
35	GABPA	chr19:40854059-40854682	HL-60	blood:	n/a	chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
36	MAX	chr19:40853509-40855470	A549	lung:	n/a	n/a
37	MAX	chr19:40854124-40854747	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr19:40854061-40854884	HUVEC	blood vessel:	n/a	n/a
39	ETS1	chr19:40854007-40854773	K562	blood:	n/a	chr19:40854299-40854310 chr19:40854258-40854269 chr19:40854314-40854327
40	GABPA	chr19:40854061-40854718	HepG2	liver:	n/a	chr19:40854690-40854699 chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
41	POLR2A	chr19:40853883-40854904	H1-neurons	neurons:	n/a	n/a
42	YY1	chr19:40854051-40854720	H1-hESC	embryonic stem cell:	n/a	chr19:40854315-40854329 chr19:40854243-40854257 chr19:40854497-40854506
43	EGR1	chr19:40854062-40854658	K562	blood:	n/a	chr19:40854262-40854272 chr19:40854581-40854590 chr19:40854213-40854223 chr19:40854244-40854254 chr19:40854205-40854219
44	GABPA	chr19:40853765-40854753	SK-N-SH	brain:	n/a	chr19:40854690-40854699 chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
45	CCNT2	chr19:40854075-40854745	K562	blood:	n/a	n/a
46	SIN3A	chr19:40853669-40855017	GM12878	blood:	n/a	chr19:40854213-40854226
47	GABPA	chr19:40853979-40854745	HL-60	blood:	n/a	chr19:40854690-40854699 chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
48	FOS	chr19:40854322-40854576	HUVEC	blood vessel:	n/a	chr19:40854527-40854536
49	GABPA	chr19:40854125-40854720	GM12878	blood:	n/a	chr19:40854690-40854699 chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
50	UBTF	chr19:40853967-40854748	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40854424-40854474	LNCaP	prostate:	n/a
2	chr19:40854409-40854459	AG10803	skin:	n/a
3	chr19:40854430-40854480	HAEpiC	amniotic membrane:	n/a
4	chr19:40854424-40854474	HIPEpiC	eye:	n/a
5	chr19:40854424-40854474	AG09319	gingival:	n/a
6	chr19:40854430-40854480	HPAEpiC	pulmonary alveolar:	n/a
7	chr19:40854430-40854480	GM12891	blood:	n/a
8	chr19:40854430-40854480	SK-N-SH	brain:	n/a
9	chr19:40854409-40854459	AG04449	skin:	fetal
10	chr19:40854430-40854480	HMEC	breast:	n/a
11	chr19:40854409-40854459	AoSMC	blood vessel:	n/a
12	chr19:40854430-40854480	Hepatocyte	liver:	n/a
13	chr19:40854430-40854480	RPTEC	kidney:	n/a
14	chr19:40854424-40854474	PANC-1	pancreas:	n/a
15	chr19:40854409-40854459	MCF-7	breast:	n/a
16	chr19:40854409-40854459	HCM	heart:	n/a
17	chr19:40854424-40854474	MCF-7	breast:	n/a
18	chr19:40854424-40854474	AoSMC	blood vessel:	n/a
19	chr19:40854430-40854480	HL-60	blood:	n/a
20	chr19:40854430-40854480	PFSK-1	brain:	n/a
21	chr19:40854424-40854474	BE2_C	brain:	n/a
22	chr19:40854424-40854474	ECC-1	luminal epithelium:	n/a
23	chr19:40854409-40854459	K562	blood:	n/a
24	chr19:40854424-40854474	Jurkat	blood:	n/a
25	chr19:40854430-40854480	AG04449	skin:	fetal
26	chr19:40854424-40854474	GM12892	blood:	n/a
27	chr19:40854424-40854474	HCPEpiC	choroid plexus:	n/a
28	chr19:40854430-40854480	MCF-7	breast:	n/a
29	chr19:40854430-40854480	NT2-D1	testis:	n/a
30	chr19:40854409-40854459	NHBE	bronchial:	n/a
31	chr19:40854409-40854459	AG09319	gingival:	n/a
32	chr19:40854430-40854480	AG09319	gingival:	n/a
33	chr19:40854424-40854474	PFSK-1	brain:	n/a
34	chr19:40854430-40854480	BJ	skin:	n/a
35	chr19:40854430-40854480	U87	brain:	n/a
36	chr19:40854409-40854459	PrEC	prostate:	n/a
37	chr19:40854424-40854474	PrEC	prostate:	n/a
38	chr19:40854430-40854480	HCPEpiC	choroid plexus:	n/a
39	chr19:40854409-40854459	GM12892	blood:	n/a
40	chr19:40854424-40854474	AG10803	skin:	n/a
41	chr19:40854409-40854459	HEK293	kidney:	embryo
42	chr19:40854424-40854474	NB4	blood:	n/a
43	chr19:40854430-40854480	HRPEpiC	eye:	n/a
44	chr19:40854424-40854474	HAEpiC	amniotic membrane:	n/a
45	chr19:40854424-40854474	NHDF-neo	bronchial:	n/a
46	chr19:40854430-40854480	HRCEpiC	kidney:	n/a
47	chr19:40854424-40854474	AG09309	skin:	n/a
48	chr19:40854409-40854459	SK-N-MC	brain:	n/a
49	chr19:40854409-40854459	ovcar-3	ovarian:	n/a
50	chr19:40854424-40854474	SK-N-SH_RA	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:
2	chr19:40853951..40856077-chr19:40931313..40932883,2	MCF-7	breast:
3	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
4	chr19:40853841..40855507-chr19:41105833..41108523,2	K562	blood:
5	chr19:40853028..40855563-chr19:40876148..40878218,2	K562	blood:
6	chr19:40853787..40856715-chr19:40882110..40885015,2	K562	blood:
7	chr19:40852692..40855852-chr19:40948280..40952207,5	K562	blood:
8	chr19:40853920..40856703-chr19:40862603..40866302,4	K562	blood:
9	chr19:40846573..40849159-chr19:40852803..40855284,3	K562	blood:
10	chr19:40853029..40856025-chr19:41082472..41085390,2	K562	blood:
11	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLD3-1	chr19:40854414-40854631	NONHSAT066374

Variant related genes	Relation type
C19orf47	TF binding region
PLD3	TF binding region
C19orf47	CpG island
PLD3	CpG island
ENSG00000167565	Chromatin interaction
ENSG00000206925	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000160410	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11666690	0.85[EUR][1000 genomes]
rs11666860	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667443	0.85[EUR][1000 genomes]
rs11667768	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668006	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11668520	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11669006	0.85[EUR][1000 genomes]
rs11669332	0.85[EUR][1000 genomes]
rs11670323	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671439	0.84[EUR][1000 genomes]
rs35090721	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3760636	0.81[ASN][1000 genomes]
rs45441197	0.93[ASN][1000 genomes]
rs45497695	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56672337	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59058760	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59106111	0.84[EUR][1000 genomes]
rs6508937	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66623822	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67587726	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245751	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933236	0.82[EUR][1000 genomes]
rs73933237	0.85[EUR][1000 genomes]
rs73933238	0.84[EUR][1000 genomes]
rs73933240	0.85[EUR][1000 genomes]
rs73933241	0.85[EUR][1000 genomes]
rs8105478	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr19:40852800-40855200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:40852800-40855200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr19:40852800-40855200	Active TSS	NHDF-Ad	bronchial
4	chr19:40852800-40855600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:40852800-40855600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:40853000-40854800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:40853000-40855000	Active TSS	NH-A	brain
8	chr19:40853000-40855200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:40853000-40855200	Active TSS	HSMM	muscle
10	chr19:40853000-40855800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:40853200-40855000	Active TSS	HMEC	breast
12	chr19:40853200-40855200	Active TSS	GM12878-XiMat	blood
13	chr19:40853200-40855200	Active TSS	K562	blood
14	chr19:40853200-40855200	Active TSS	NHLF	lung
15	chr19:40853200-40855400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40853400-40855000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:40853400-40855000	Active TSS	Fetal Lung	lung
18	chr19:40853400-40855000	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:40853400-40855000	Active TSS	HSMMtube	muscle
20	chr19:40853400-40855200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:40853400-40855200	Active TSS	Fetal Muscle Trunk	muscle
22	chr19:40853400-40855400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr19:40853400-40855600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:40853400-40855600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr19:40853400-40855600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:40853600-40854600	Active TSS	Brain Germinal Matrix	brain
27	chr19:40853600-40854800	Active TSS	Primary T cells from cord blood	blood
28	chr19:40853600-40855000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:40853600-40855000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:40853600-40855000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr19:40853600-40855200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:40853600-40855200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:40853600-40855200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:40853600-40855200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:40853600-40855200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:40853600-40855200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:40853600-40855200	Active TSS	Fetal Intestine Small	intestine
38	chr19:40853600-40855200	Active TSS	Left Ventricle	heart
39	chr19:40853600-40855200	Active TSS	Lung	lung
40	chr19:40853600-40855200	Active TSS	Ovary	ovary
41	chr19:40853600-40855200	Active TSS	Pancreas	Pancrea
42	chr19:40853600-40855200	Active TSS	Right Ventricle	heart
43	chr19:40853600-40855200	Active TSS	Small Intestine	intestine
44	chr19:40853600-40855200	Active TSS	A549	lung
45	chr19:40853600-40855400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr19:40853600-40855400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr19:40853600-40855400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:40853600-40855400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:40853600-40855400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:40853600-40855400	Active TSS	Aorta	Aorta

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