Variant report

Variant	rs1792199
Chromosome Location	chr11:73588570-73588571
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	chr11:73587397-73588622	GM19099	blood:	n/a	n/a
2	MXI1	chr11:73586246-73588801	SK-N-SH	brain:	n/a	n/a
3	MAX	chr11:73587160-73588629	HepG2	liver:	n/a	chr11:73587946-73587954
4	MAFK	chr11:73588255-73588577	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:73585876-73588793	SK-N-MC	brain:	n/a	n/a
6	E2F4	chr11:73587446-73588660	MCF10A-Er-Src	breast:	n/a	chr11:73587721-73587730 chr11:73588052-73588061
7	POLR2A	chr11:73587420-73588589	NB4	blood:	n/a	n/a
8	MYC	chr11:73586428-73588664	A549	lung:	n/a	chr11:73587946-73587954
9	NRF1	chr11:73587289-73588638	SK-N-SH	brain:	n/a	chr11:73587720-73587731 chr11:73587729-73587738 chr11:73587731-73587742 chr11:73587720-73587731 chr11:73587722-73587731 chr11:73587720-73587734
10	TEAD4	chr11:73586761-73588604	K562	blood:	n/a	n/a
11	PML	chr11:73587415-73588577	MCF-7	breast:	n/a	n/a
12	POLR2A	chr11:73587306-73588592	GM12892	blood:	n/a	n/a
13	MAX	chr11:73587430-73588596	HepG2	liver:	n/a	chr11:73587946-73587954
14	REST	chr11:73587100-73588808	H1-neurons	neurons:	n/a	n/a
15	MAX	chr11:73587220-73588683	A549	lung:	n/a	chr11:73587946-73587954
16	GABPA	chr11:73587376-73588575	SK-N-SH	brain:	n/a	chr11:73587720-73587731 chr11:73587729-73587738 chr11:73587722-73587731 chr11:73587720-73587734
17	TCF7L2	chr11:73587297-73588634	HEK293	kidney:	n/a	chr11:73587705-73587715
18	MAX	chr11:73587190-73588617	HCT-116	colon:	n/a	chr11:73587946-73587954
19	GABPA	chr11:73587099-73588663	MCF-7	breast:	n/a	chr11:73587720-73587731 chr11:73587729-73587738 chr11:73587722-73587731 chr11:73587720-73587734
20	TCF12	chr11:73587248-73588637	A549	lung:	n/a	n/a
21	POLR2A	chr11:73586645-73588995	HepG2	liver:	n/a	n/a
22	POLR2A	chr11:73586794-73588654	Hela-S3	cervix:	n/a	n/a
23	MXI1	chr11:73586863-73588875	IMR90	lung:	n/a	n/a
24	POLR2A	chr11:73586700-73588786	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr11:73586724-73588590	GM12892	blood:	n/a	n/a
26	POLR2A	chr11:73587306-73588699	K562	blood:	n/a	n/a
27	GABPA	chr11:73587462-73588605	SK-N-SH	brain:	n/a	chr11:73587720-73587731 chr11:73587729-73587738 chr11:73587722-73587731 chr11:73587720-73587734
28	SIN3AK20	chr11:73587195-73588724	MCF-7	breast:	n/a	n/a
29	GABPA	chr11:73587295-73588603	A549	lung:	n/a	chr11:73587720-73587731 chr11:73587729-73587738 chr11:73587722-73587731 chr11:73587720-73587734
30	MYC	chr11:73587465-73588602	Hela-S3	cervix:	n/a	chr11:73587946-73587954
31	POLR2A	chr11:73587252-73588682	HUVEC	blood vessel:	n/a	n/a
32	TCF7L2	chr11:73587358-73588742	Hela-S3	cervix:	n/a	chr11:73587705-73587715
33	POLR2A	chr11:73587245-73588630	HL-60	blood:	n/a	n/a
34	GTF2F1	chr11:73587478-73588639	Hela-S3	cervix:	n/a	n/a
35	TCF7L2	chr11:73587374-73588627	PANC-1	pancreas:	n/a	chr11:73587705-73587715
36	HCFC1	chr11:73586850-73588832	Hela-S3	cervix:	n/a	n/a
37	PML	chr11:73587323-73588665	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:73586144-73588619	GM12891	blood:	n/a	n/a
39	POLR2A	chr11:73587450-73588573	K562	blood:	n/a	n/a
40	POLR2A	chr11:73587060-73588672	MCF10A-Er-Src	breast:	n/a	n/a
41	MAFF	chr11:73588066-73588603	K562	blood:	n/a	n/a
42	POLR2A	chr11:73587424-73588582	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:73588532-73588582	HepG2	liver:	n/a
2	chr11:73588532-73588582	HEK293	kidney:	embryo
3	chr11:73588532-73588582	NHDF-neo	bronchial:	n/a
4	chr11:73588532-73588582	GM12891	blood:	n/a
5	chr11:73588532-73588582	AG04449	skin:	fetal
6	chr11:73588532-73588582	HNPCEpiC	eye:	n/a
7	chr11:73588532-73588582	Caco-2	colon:	n/a
8	chr11:73588532-73588582	HRE	kidney:	n/a
9	chr11:73588532-73588582	MCF10A-Er-Src	breast:	n/a
10	chr11:73588532-73588582	Jurkat	blood:	n/a
11	chr11:73588532-73588582	H1-hESC	embryonic stem cell:	embryo
12	chr11:73588532-73588582	HRCEpiC	kidney:	n/a
13	chr11:73588532-73588582	NB4	blood:	n/a
14	chr11:73588532-73588582	ProgFib	skin:	n/a
15	chr11:73588532-73588582	AG09309	skin:	n/a
16	chr11:73588532-73588582	MCF-7	breast:	n/a
17	chr11:73588532-73588582	SAEC	small airway:	n/a
18	chr11:73588532-73588582	GM19239	blood:	n/a
19	chr11:73588532-73588582	HEEpiC	esophagus:	n/a
20	chr11:73588532-73588582	SK-N-SH	brain:	n/a
21	chr11:73588532-73588582	PANC-1	pancreas:	n/a
22	chr11:73588532-73588582	ovcar-3	ovarian:	n/a
23	chr11:73588532-73588582	CMK	blood:	n/a
24	chr11:73588532-73588582	GM12892	blood:	n/a
25	chr11:73588532-73588582	NT2-D1	testis:	n/a
26	chr11:73588532-73588582	SK-N-MC	brain:	n/a
27	chr11:73588532-73588582	HCT-116	colon:	n/a
28	chr11:73588532-73588582	PFSK-1	brain:	n/a
29	chr11:73588532-73588582	BE2_C	brain:	n/a
30	chr11:73588532-73588582	HL-60	blood:	n/a
31	chr11:73588532-73588582	IMR90	lung:	fetal
32	chr11:73588532-73588582	K562	blood:	n/a
33	chr11:73588532-73588582	GM06990	blood:	n/a
34	chr11:73588532-73588582	RPTEC	kidney:	n/a
35	chr11:73588532-73588582	T-47D	breast:	n/a
36	chr11:73588532-73588582	BJ	skin:	n/a
37	chr11:73588532-73588582	LNCaP	prostate:	n/a
38	chr11:73588532-73588582	AoSMC	blood vessel:	n/a
39	chr11:73588532-73588582	PrEC	prostate:	n/a
40	chr11:73588532-73588582	HMEC	breast:	n/a
41	chr11:73588532-73588582	U87	brain:	n/a
42	chr11:73588532-73588582	NH-A	brain:	n/a
43	chr11:73588532-73588582	ECC-1	luminal epithelium:	n/a
44	chr11:73588532-73588582	HCF	heart:	n/a
45	chr11:73588532-73588582	AG10803	skin:	n/a
46	chr11:73588532-73588582	AG09319	gingival:	n/a
47	chr11:73588532-73588582	HCPEpiC	choroid plexus:	n/a
48	chr11:73588532-73588582	HPAEpiC	pulmonary alveolar:	n/a
49	chr11:73588532-73588582	HIPEpiC	eye:	n/a
50	chr11:73588532-73588582	SK-N-SH_RA	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73587992..73588608-chr12:51441696..51442224,2	Hela-S3	cervix:
2	chr11:73497005..73500757-chr11:73586552..73589226,3	MCF-7	breast:
3	chr11:73561146..73563311-chr11:73588199..73589761,2	K562	blood:
4	chr11:73496600..73498927-chr11:73587563..73589388,3	MCF-7	breast:
5	chr11:73101451..73103302-chr11:73587436..73589979,2	MCF-7	breast:
6	chr11:73587462..73590069-chr11:73692817..73694652,2	K562	blood:
7	chr11:73586922..73589181-chr11:73687473..73690308,2	K562	blood:
8	chr11:73371085..73373574-chr11:73587519..73589689,2	MCF-7	breast:
9	chr11:73470519..73472838-chr11:73586575..73589489,2	MCF-7	breast:
10	chr11:73586195..73589455-chr11:73595184..73599458,5	K562	blood:
11	chr1:45196591..45197186-chr11:73587825..73588807,2	Hela-S3	cervix:
12	chr11:73497934..73501442-chr11:73586433..73589232,4	K562	blood:
13	chr11:73497415..73503223-chr11:73585602..73589591,8	K562	blood:
14	chr11:73585766..73589510-chr11:73599101..73602813,5	MCF-7	breast:

Variant related genes	Relation type
COA4	TF binding region
PAAF1	TF binding region
PAAF1	CpG island
COA4	CpG island
ENSG00000175582	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000256034	Chromatin interaction
ENSG00000256681	Chromatin interaction
ENSG00000175581	Chromatin interaction
ENSG00000175575	Chromatin interaction
ENSG00000175567	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000054967	Chromatin interaction
ENSG00000021300	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10898948	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10898950	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11220	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235932	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs1670543	0.83[GIH][hapmap]
rs1670545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1670546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1670557	0.81[GIH][hapmap]
rs1670558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792198	0.83[GIH][hapmap]
rs3018335	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4362170	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs935985	0.84[MEX][hapmap]
rs935988	0.84[MEX][hapmap]

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	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers 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 target site	47 gene(s)	inside rSNPs	diseases
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1792199	RNF121	cis	cerebellum	SCAN
rs1792199	PAAF1	cis	Lymphoblastoid	GTEx
rs1792199	C11orf59	cis	parietal	SCAN
rs1792199	FLJ11848	cis	multi-tissue	Pritchard
rs1792199	PAAF1	cis	lymphoblastoid	seeQTL
rs1792199	OMP	cis	parietal	SCAN
rs1792199	MRPL48	cis	parietal	SCAN
rs1792199	PAAF1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73586400-73588800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr11:73586600-73588600	Active TSS	Fetal Intestine Small	intestine
3	chr11:73586600-73588600	Active TSS	Fetal Muscle Trunk	muscle
4	chr11:73586600-73588800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr11:73586600-73588800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr11:73586600-73588800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:73586600-73588800	Active TSS	A549	lung
8	chr11:73586600-73588800	Active TSS	HMEC	breast
9	chr11:73586600-73589000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:73586600-73589600	Active TSS	GM12878-XiMat	blood
11	chr11:73586800-73588600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:73586800-73588600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:73586800-73588800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr11:73586800-73588800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr11:73586800-73588800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:73586800-73588800	Active TSS	NHDF-Ad	bronchial
17	chr11:73587000-73588600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr11:73587000-73588600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:73587000-73588600	Active TSS	Fetal Intestine Large	intestine
20	chr11:73587000-73588600	Active TSS	Fetal Kidney	kidney
21	chr11:73587000-73588600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr11:73587000-73588600	Active TSS	Gastric	stomach
23	chr11:73587000-73588800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr11:73587000-73588800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:73587000-73588800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:73587000-73588800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr11:73587000-73588800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:73587000-73588800	Active TSS	Psoas Muscle	Psoas
29	chr11:73587000-73589000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:73587000-73589000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:73587000-73589000	Active TSS	HSMM	muscle
32	chr11:73587000-73589200	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr11:73587000-73589200	Active TSS	K562	blood
34	chr11:73587000-73589400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:73587200-73588600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr11:73587200-73588600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:73587200-73588600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:73587200-73588600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:73587200-73588600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:73587200-73588600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr11:73587200-73588600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:73587200-73588600	Active TSS	Aorta	Aorta
43	chr11:73587200-73588600	Active TSS	Brain Hippocampus Middle	brain
44	chr11:73587200-73588600	Active TSS	Esophagus	oesophagus
45	chr11:73587200-73588600	Active TSS	Fetal Heart	heart
46	chr11:73587200-73588600	Active TSS	Fetal Stomach	stomach
47	chr11:73587200-73588600	Active TSS	Left Ventricle	heart
48	chr11:73587200-73588600	Active TSS	Lung	lung
49	chr11:73587200-73588600	Active TSS	Ovary	ovary
50	chr11:73587200-73588800	Active TSS	H1 Cell Line	embryonic stem cell

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