Variant report

Variant	rs11799363
Chromosome Location	chr1:224180489-224180490
allele	C/T
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	CREB1	chr1:224180170-224180518	GM12878	blood:	n/a	chr1:224180368-224180381 chr1:224180343-224180356
2	POLR2A	chr1:224179744-224180784	PFSK-1	brain:	n/a	n/a
3	SP1	chr1:224179925-224180815	HepG2	liver:	n/a	chr1:224180308-224180319 chr1:224180399-224180420
4	SP1	chr1:224180020-224180579	K562	blood:	n/a	chr1:224180308-224180319 chr1:224180399-224180420
5	POLR2A	chr1:224179691-224180920	GM12878	blood:	n/a	n/a
6	NR3C1	chr1:224179981-224180917	A549	lung:	n/a	chr1:224180049-224180063
7	FOXM1	chr1:224179950-224180608	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:224178488-224181742	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIX5	chr1:224179719-224180580	K562	blood:	n/a	n/a
10	JUND	chr1:224180061-224180764	HepG2	liver:	n/a	chr1:224180402-224180411 chr1:224180345-224180354
11	NFIC	chr1:224179796-224180591	GM12878	blood:	n/a	n/a
12	CREB1	chr1:224180190-224180506	ECC-1	luminal epithelium:	n/a	chr1:224180368-224180381 chr1:224180343-224180356
13	SP1	chr1:224180120-224180498	H1-hESC	embryonic stem cell:	n/a	chr1:224180308-224180319 chr1:224180399-224180420
14	REST	chr1:224180389-224180784	H1-hESC	embryonic stem cell:	n/a	chr1:224180725-224180743 chr1:224180701-224180714
15	FOXP2	chr1:224180168-224180509	PFSK-1	brain:	n/a	n/a
16	SRF	chr1:224180171-224180530	K562	blood:	n/a	n/a
17	CREB1	chr1:224180140-224180501	A549	lung:	n/a	chr1:224180368-224180381 chr1:224180343-224180356
18	POLR2A	chr1:224178929-224180943	GM12892	blood:	n/a	n/a
19	MAX	chr1:224180137-224180594	K562	blood:	n/a	n/a
20	POLR2A	chr1:224180045-224180858	GM19099	blood:	n/a	n/a
21	JUND	chr1:224180119-224180567	K562	blood:	n/a	chr1:224180402-224180411 chr1:224180345-224180354
22	JUND	chr1:224180212-224180569	A549	lung:	n/a	chr1:224180402-224180411 chr1:224180345-224180354
23	POLR2A	chr1:224179905-224180798	A549	lung:	n/a	n/a
24	TAF1	chr1:224179838-224180875	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:224179842-224181001	U87	brain:	n/a	n/a
26	IRF1	chr1:224180168-224180553	K562	blood:	n/a	n/a
27	POLR2A	chr1:224180053-224180657	HEK293	kidney:	n/a	n/a
28	EP300	chr1:224180135-224180509	SK-N-SH_RA	brain:	n/a	n/a
29	EP300	chr1:224179867-224180741	GM12878	blood:	n/a	chr1:224180533-224180542
30	IRF1	chr1:224180191-224180567	K562	blood:	n/a	n/a
31	POLR2A	chr1:224180019-224180797	Hela-S3	cervix:	n/a	n/a
32	MXI1	chr1:224179912-224180773	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr1:224180046-224180652	K562	blood:	n/a	n/a
34	CHD2	chr1:224180101-224180490	GM12878	blood:	n/a	n/a
35	RXRA	chr1:224180287-224180870	HepG2	liver:	n/a	n/a
36	PML	chr1:224180086-224180732	GM12878	blood:	n/a	n/a
37	NFYB	chr1:224180205-224180580	GM12878	blood:	n/a	chr1:224180395-224180410 chr1:224180398-224180413 chr1:224180398-224180412 chr1:224180398-224180413
38	MAZ	chr1:224180118-224180600	K562	blood:	n/a	n/a
39	NFYB	chr1:224180235-224180577	Hela-S3	cervix:	n/a	chr1:224180395-224180410 chr1:224180398-224180413 chr1:224180398-224180412 chr1:224180398-224180413
40	CTCF	chr1:224180459-224180544	GM12891	blood:	n/a	n/a
41	GATA2	chr1:224179742-224180837	K562	blood:	n/a	n/a
42	EBF1	chr1:224180027-224180661	GM12878	blood:	n/a	n/a
43	ZBTB33	chr1:224180451-224180824	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:224180047-224180765	GM19193	blood:	n/a	n/a
45	MAZ	chr1:224180227-224180558	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:224180043-224180884	Hela-S3	cervix:	n/a	n/a
47	SIX5	chr1:224180078-224180650	A549	lung:	n/a	n/a
48	POLR2A	chr1:224180057-224180606	GM10847	blood:	n/a	n/a
49	MAX	chr1:224180103-224180554	K562	blood:	n/a	n/a
50	SIN3AK20	chr1:224180126-224180570	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:224180444-224180494	HCM	heart:	n/a
2	chr1:224180444-224180494	AG09309	skin:	n/a
3	chr1:224180444-224180494	GM12891	blood:	n/a
4	chr1:224180444-224180494	MCF-7	breast:	n/a
5	chr1:224180444-224180494	GM12878	blood:	n/a
6	chr1:224180444-224180494	GM12892	blood:	n/a
7	chr1:224180444-224180494	HRE	kidney:	n/a
8	chr1:224180444-224180494	SAEC	small airway:	n/a
9	chr1:224180444-224180494	GM06990	blood:	n/a
10	chr1:224180444-224180494	AG09319	gingival:	n/a
11	chr1:224180444-224180494	AG10803	skin:	n/a
12	chr1:224180444-224180494	A549	lung:	n/a
13	chr1:224180444-224180494	NT2-D1	testis:	n/a
14	chr1:224180444-224180494	SK-N-SH_RA	brain:	n/a
15	chr1:224180444-224180494	AoSMC	blood vessel:	n/a
16	chr1:224180444-224180494	HRCEpiC	kidney:	n/a
17	chr1:224180444-224180494	HCPEpiC	choroid plexus:	n/a
18	chr1:224180444-224180494	PANC-1	pancreas:	n/a
19	chr1:224180444-224180494	NH-A	brain:	n/a
20	chr1:224180444-224180494	HCF	heart:	n/a
21	chr1:224180444-224180494	HCT-116	colon:	n/a
22	chr1:224180444-224180494	Caco-2	colon:	n/a
23	chr1:224180444-224180494	AG04449	skin:	fetal
24	chr1:224180444-224180494	U87	brain:	n/a
25	chr1:224180444-224180494	HIPEpiC	eye:	n/a
26	chr1:224180444-224180494	K562	blood:	n/a
27	chr1:224180444-224180494	Hepatocyte	liver:	n/a
28	chr1:224180444-224180494	HRPEpiC	eye:	n/a
29	chr1:224180444-224180494	ECC-1	luminal epithelium:	n/a
30	chr1:224180444-224180494	T-47D	breast:	n/a
31	chr1:224180444-224180494	HNPCEpiC	eye:	n/a
32	chr1:224180444-224180494	PrEC	prostate:	n/a
33	chr1:224180444-224180494	Jurkat	blood:	n/a
34	chr1:224180444-224180494	HEK293	kidney:	embryo
35	chr1:224180444-224180494	SKMC	muscle:	n/a
36	chr1:224180444-224180494	GM19239	blood:	n/a
37	chr1:224180444-224180494	SK-N-SH	brain:	n/a
38	chr1:224180444-224180494	HEEpiC	esophagus:	n/a
39	chr1:224180444-224180494	HAEpiC	amniotic membrane:	n/a
40	chr1:224180444-224180494	AG04450	lung:	fetal
41	chr1:224180444-224180494	LNCaP	prostate:	n/a
42	chr1:224180444-224180494	HL-60	blood:	n/a
43	chr1:224180444-224180494	HMEC	breast:	n/a
44	chr1:224180444-224180494	IMR90	lung:	fetal
45	chr1:224180444-224180494	BE2_C	brain:	n/a
46	chr1:224180444-224180494	MCF10A-Er-Src	breast:	n/a
47	chr1:224180444-224180494	HepG2	liver:	n/a
48	chr1:224180444-224180494	CMK	blood:	n/a
49	chr1:224180444-224180494	ovcar-3	ovarian:	n/a
50	chr1:224180444-224180494	PFSK-1	brain:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224178733..224180652-chr1:224310129..224312087,2	K562	blood:
2	chr1:224178905..224181889-chr1:224301318..224303879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185495	TF binding region
ENSG00000232372	TF binding region
ENSG00000243000	TF binding region
ENSG00000185495	CpG island
ENSG00000232372	CpG island
ENSG00000243000	CpG island
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs61826603	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv873215	chr1:224075483-224204433	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv873216	chr1:224075483-224230307	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv1802502	chr1:224076065-224184733	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv873217	chr1:224089383-224190316	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv873218	chr1:224097155-224204433	Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv873219	chr1:224097155-224216822	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv873220	chr1:224097155-224223659	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv549241	chr1:224103992-224216757	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv873221	chr1:224115297-224183599	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv549242	chr1:224115297-224203918	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv549243	chr1:224115297-224216757	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv945316	chr1:224133366-224196526	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv947070	chr1:224178779-224183075	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11799363	RP11-504P24.6	cis	Nerve Tibial	GTEx
rs11799363	RP11-504P24.4	cis	Thyroid	GTEx
rs11799363	RP11-504P24.4	cis	Nerve Tibial	GTEx
rs11799363	RP11-504P24.6	cis	Thyroid	GTEx
rs11799363	RP11-504P24.3	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224179000-224182200	Active TSS	GM12878-XiMat	blood
2	chr1:224179200-224181800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224179400-224181400	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:224179400-224182200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:224179600-224181400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:224179600-224181400	Active TSS	Brain Hippocampus Middle	brain
7	chr1:224179600-224181400	Active TSS	Fetal Muscle Leg	muscle
8	chr1:224179600-224181400	Active TSS	Dnd41	blood
9	chr1:224179600-224181400	Active TSS	NHEK	skin
10	chr1:224179600-224181600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:224179600-224181600	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr1:224179600-224181600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:224179600-224181600	Active TSS	Brain Angular Gyrus	brain
14	chr1:224179600-224181600	Active TSS	Fetal Intestine Large	intestine
15	chr1:224179600-224181600	Active TSS	A549	lung
16	chr1:224179600-224181600	Active TSS	HMEC	breast
17	chr1:224179600-224181600	Active TSS	HSMM	muscle
18	chr1:224179600-224181600	Active TSS	K562	blood
19	chr1:224179600-224181800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:224179600-224181800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:224179600-224181800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:224179600-224181800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:224179600-224181800	Active TSS	Fetal Intestine Small	intestine
24	chr1:224179600-224181800	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:224179600-224182200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:224179600-224182200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:224179600-224182200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:224179600-224182200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:224179600-224182200	Active TSS	Osteobl	bone
30	chr1:224179600-224182400	Active TSS	HepG2	liver
31	chr1:224179800-224181000	Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr1:224179800-224181000	Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr1:224179800-224181000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:224179800-224181200	Active TSS	Primary B cells from peripheral blood	blood
35	chr1:224179800-224181200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr1:224179800-224181200	Active TSS	Psoas Muscle	Psoas
37	chr1:224179800-224181400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:224179800-224181400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:224179800-224181400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr1:224179800-224181400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:224179800-224181400	Active TSS	Primary T cells from cord blood	blood
42	chr1:224179800-224181400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:224179800-224181400	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:224179800-224181400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:224179800-224181400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr1:224179800-224181400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr1:224179800-224181400	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:224179800-224181400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr1:224179800-224181400	Active TSS	Fetal Lung	lung
50	chr1:224179800-224181400	Active TSS	Placenta	Placenta

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