Variant report

Variant	rs1001179
Chromosome Location	chr11:34460231-34460232
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	chr11:34460028-34461065	Hela-S3	cervix:	n/a	n/a
2	SP1	chr11:34459937-34460711	K562	blood:	n/a	chr11:34460209-34460218 chr11:34460419-34460431 chr11:34460419-34460431 chr11:34460416-34460430 chr11:34460421-34460430 chr11:34460208-34460220 chr11:34460420-34460429 chr11:34460392-34460413 chr11:34460208-34460220
3	TAF1	chr11:34460062-34461020	ECC-1	luminal epithelium:	n/a	n/a
4	ZNF143	chr11:34460181-34461165	GM12878	blood:	n/a	n/a
5	ELK1	chr11:34460182-34460881	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:34459976-34461418	GM12891	blood:	n/a	n/a
7	ETS1	chr11:34460002-34460468	K562	blood:	n/a	chr11:34460201-34460210
8	POLR2A	chr11:34459881-34460731	K562	blood:	n/a	n/a
9	CEBPB	chr11:34460092-34461116	Hela-S3	cervix:	n/a	chr11:34460394-34460402 chr11:34460444-34460452
10	PML	chr11:34459936-34461412	GM12878	blood:	n/a	n/a
11	HDAC2	chr11:34460071-34460429	K562	blood:	n/a	n/a
12	YY1	chr11:34460053-34461132	GM12892	blood:	n/a	n/a
13	RAD21	chr11:34460031-34460372	K562	blood:	n/a	chr11:34460237-34460250
14	NFYA	chr11:34460097-34460634	GM12878	blood:	n/a	chr11:34460393-34460403 chr11:34460390-34460402 chr11:34460441-34460455 chr11:34460391-34460409 chr11:34460436-34460454 chr11:34460391-34460405 chr11:34460391-34460404 chr11:34460391-34460406 chr11:34460440-34460455 chr11:34460443-34460453 chr11:34460391-34460406 chr11:34460444-34460456 chr11:34460440-34460455
15	MAX	chr11:34460070-34460770	SK-N-SH	brain:	n/a	chr11:34460418-34460428
16	POLR2A	chr11:34460017-34460772	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr11:34460048-34461033	GM15510	blood:	n/a	n/a
18	POLR2A	chr11:34460026-34461136	PFSK-1	brain:	n/a	n/a
19	CHD2	chr11:34460053-34461093	Hela-S3	cervix:	n/a	n/a
20	ATF2	chr11:34460173-34460659	GM12878	blood:	n/a	n/a
21	GTF2F1	chr11:34460012-34461130	Hela-S3	cervix:	n/a	n/a
22	PML	chr11:34459903-34460929	K562	blood:	n/a	n/a
23	SIN3AK20	chr11:34460001-34461037	MCF-7	breast:	n/a	n/a
24	RFX5	chr11:34460117-34461098	HepG2	liver:	n/a	chr11:34460443-34460452 chr11:34460394-34460403
25	EP300	chr11:34460141-34460691	T-47D	breast:	n/a	chr11:34460168-34460184
26	GATA2	chr11:34459959-34460471	K562	blood:	n/a	chr11:34460195-34460204
27	TBP	chr11:34459858-34460643	Hela-S3	cervix:	n/a	n/a
28	PML	chr11:34459919-34461024	K562	blood:	n/a	n/a
29	POLR2A	chr11:34460054-34460718	A549	lung:	n/a	n/a
30	POLR2A	chr11:34459911-34461035	U87	brain:	n/a	n/a
31	ZBTB7A	chr11:34460037-34460991	K562	blood:	n/a	n/a
32	E2F6	chr11:34460061-34460976	A549	lung:	n/a	chr11:34460393-34460402 chr11:34460444-34460453 chr11:34460245-34460254 chr11:34460420-34460432
33	FOS	chr11:34460137-34460623	K562	blood:	n/a	chr11:34460395-34460404 chr11:34460442-34460451
34	ELK1	chr11:34459944-34461069	GM12878	blood:	n/a	n/a
35	MYC	chr11:34460045-34461208	NB4	blood:	n/a	chr11:34460418-34460428
36	MAZ	chr11:34459884-34461417	IMR90	lung:	n/a	chr11:34460418-34460428
37	POLR2A	chr11:34460013-34460660	SK-N-SH	brain:	n/a	n/a
38	MXI1	chr11:34459837-34461252	IMR90	lung:	n/a	n/a
39	YY1	chr11:34460078-34460739	A549	lung:	n/a	n/a
40	YY1	chr11:34460102-34461027	HepG2	liver:	n/a	n/a
41	POLR2A	chr11:34459962-34460862	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr11:34460135-34460833	MCF-7	breast:	n/a	n/a
43	POLR2A	chr11:34460044-34461154	Raji	blood:	n/a	n/a
44	MAX	chr11:34460222-34460927	MCF-7	breast:	n/a	chr11:34460418-34460428
45	SP2	chr11:34460190-34460529	K562	blood:	n/a	chr11:34460415-34460430 chr11:34460394-34460404
46	POLR2A	chr11:34459916-34460968	K562	blood:	n/a	n/a
47	RELA	chr11:34459995-34461452	GM15510	blood:	n/a	n/a
48	POLR2A	chr11:34459983-34461177	GM12878	blood:	n/a	n/a
49	BHLHE40	chr11:34460063-34461082	K562	blood:	n/a	n/a
50	CBX3	chr11:34459990-34460375	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:34460182-34460232	SK-N-SH	brain:	n/a
2	chr11:34460182-34460232	HL-60	blood:	n/a
3	chr11:34460182-34460232	PANC-1	pancreas:	n/a
4	chr11:34460182-34460232	Jurkat	blood:	n/a
5	chr11:34460182-34460232	LNCaP	prostate:	n/a
6	chr11:34460182-34460232	U87	brain:	n/a
7	chr11:34460182-34460232	CMK	blood:	n/a
8	chr11:34460182-34460232	AG04449	skin:	fetal
9	chr11:34460182-34460232	HRE	kidney:	n/a
10	chr11:34460182-34460232	AG10803	skin:	n/a
11	chr11:34460182-34460232	HCPEpiC	choroid plexus:	n/a
12	chr11:34460182-34460232	AG09309	skin:	n/a
13	chr11:34460182-34460232	HMEC	breast:	n/a
14	chr11:34460182-34460232	PrEC	prostate:	n/a
15	chr11:34460182-34460232	HRCEpiC	kidney:	n/a
16	chr11:34460182-34460232	BJ	skin:	n/a
17	chr11:34460182-34460232	SK-N-SH_RA	brain:	n/a
18	chr11:34460182-34460232	AoSMC	blood vessel:	n/a
19	chr11:34460182-34460232	HEK293	kidney:	embryo
20	chr11:34460182-34460232	MCF-7	breast:	n/a
21	chr11:34460182-34460232	HAEpiC	amniotic membrane:	n/a
22	chr11:34460182-34460232	GM12892	blood:	n/a
23	chr11:34460182-34460232	GM19239	blood:	n/a
24	chr11:34460182-34460232	HPAEpiC	pulmonary alveolar:	n/a
25	chr11:34460182-34460232	HIPEpiC	eye:	n/a
26	chr11:34460182-34460232	RPTEC	kidney:	n/a
27	chr11:34460182-34460232	MCF10A-Er-Src	breast:	n/a
28	chr11:34460182-34460232	K562	blood:	n/a
29	chr11:34460182-34460232	HUVEC	blood vessel:	n/a
30	chr11:34460182-34460232	Caco-2	colon:	n/a
31	chr11:34460182-34460232	IMR90	lung:	fetal
32	chr11:34460182-34460232	HepG2	liver:	n/a
33	chr11:34460182-34460232	HNPCEpiC	eye:	n/a
34	chr11:34460182-34460232	AG04450	lung:	fetal
35	chr11:34460182-34460232	HRPEpiC	eye:	n/a
36	chr11:34460182-34460232	HEEpiC	esophagus:	n/a
37	chr11:34460182-34460232	GM12878	blood:	n/a
38	chr11:34460182-34460232	ProgFib	skin:	n/a
39	chr11:34460182-34460232	BE2_C	brain:	n/a
40	chr11:34460182-34460232	ECC-1	luminal epithelium:	n/a
41	chr11:34460182-34460232	AG09319	gingival:	n/a
42	chr11:34460182-34460232	ovcar-3	ovarian:	n/a
43	chr11:34460182-34460232	NT2-D1	testis:	n/a
44	chr11:34460182-34460232	H1-hESC	embryonic stem cell:	embryo
45	chr11:34460182-34460232	SAEC	small airway:	n/a
46	chr11:34460182-34460232	SK-N-MC	brain:	n/a
47	chr11:34460182-34460232	GM06990	blood:	n/a
48	chr11:34460182-34460232	A549	lung:	n/a
49	chr11:34460182-34460232	NB4	blood:	n/a
50	chr11:34460182-34460232	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34452352..34457130-chr11:34458043..34461797,6	K562	blood:
2	chr11:34459889..34460514-chr19:55918676..55919523,2	Hela-S3	cervix:

Variant related genes	Relation type
CAT	TF binding region
CAT	CpG island
ENSG00000108106	Chromatin interaction
ENSG00000216708	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10836234	1.00[CHD][hapmap];0.87[MEX][hapmap]
rs11032654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap]
rs11032695	1.00[CHD][hapmap];0.87[MEX][hapmap]
rs11032718	1.00[ASN][1000 genomes]
rs11032719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11032722	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11032723	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11032724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11032728	0.90[ASN][1000 genomes]
rs11604331	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs1267468	1.00[YRI][hapmap]
rs12790145	0.90[ASN][1000 genomes]
rs12797274	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12797675	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12804506	0.88[CHD][hapmap];0.82[MEX][hapmap]
rs12804689	0.82[MEX][hapmap]
rs12807961	1.00[CHD][hapmap];0.87[MEX][hapmap]
rs12808450	1.00[CHD][hapmap];0.87[MEX][hapmap]
rs1535719	1.00[ASN][1000 genomes]
rs17269931	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2231821	0.90[ASN][1000 genomes]
rs2231825	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2231828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2476504	1.00[JPT][hapmap]
rs34234992	0.90[ASN][1000 genomes]
rs34366473	0.90[ASN][1000 genomes]
rs34901344	0.90[ASN][1000 genomes]
rs35495760	0.90[ASN][1000 genomes]
rs475043	1.00[ASN][1000 genomes]
rs4756135	1.00[YRI][hapmap]
rs494024	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs499406	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs508370	0.91[ASN][1000 genomes]
rs511895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs524167	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs533425	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs55898107	0.90[ASN][1000 genomes]
rs560807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs61880810	0.84[AFR][1000 genomes]
rs737254	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv553997	chr11:34458230-34460711	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1001179	CAT	cis	Whole Blood	GTEx
rs1001179	CAT	cis	multi-tissue	Pritchard
rs1001179	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs1001179	CAT	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34458800-34461200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:34458800-34463200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:34459000-34461600	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr11:34459200-34461000	Active TSS	Muscle Satellite Cultured Cells	--
5	chr11:34459200-34461000	Active TSS	HMEC	breast
6	chr11:34459200-34461200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr11:34459400-34461000	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr11:34459400-34461200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:34459400-34461200	Active TSS	NHDF-Ad	bronchial
10	chr11:34459400-34461600	Active TSS	K562	blood
11	chr11:34459600-34460400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr11:34459600-34460600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:34459600-34460800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:34459600-34460800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:34459600-34460800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr11:34459600-34461000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:34459600-34461000	Active TSS	Brain Cingulate Gyrus	brain
18	chr11:34459600-34461000	Active TSS	Brain Germinal Matrix	brain
19	chr11:34459600-34461000	Active TSS	Fetal Muscle Leg	muscle
20	chr11:34459600-34461000	Active TSS	HSMMtube	muscle
21	chr11:34459600-34461000	Active TSS	NH-A	brain
22	chr11:34459600-34461200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:34459600-34461200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr11:34459600-34461200	Active TSS	Fetal Brain Female	brain
25	chr11:34459600-34461200	Active TSS	Fetal Stomach	stomach
26	chr11:34459600-34461200	Active TSS	Fetal Thymus	thymus
27	chr11:34459600-34461200	Active TSS	Right Ventricle	heart
28	chr11:34459600-34461200	Active TSS	Stomach Smooth Muscle	stomach
29	chr11:34459600-34461200	Active TSS	Thymus	Thymus
30	chr11:34459600-34461200	Active TSS	NHLF	lung
31	chr11:34459600-34461400	Active TSS	Aorta	Aorta
32	chr11:34459600-34461400	Active TSS	Right Atrium	heart
33	chr11:34459600-34461600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:34459600-34461800	Active TSS	A549	lung
35	chr11:34459600-34462000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:34459600-34462000	Active TSS	Fetal Kidney	kidney
37	chr11:34459800-34460400	Enhancers	Fetal Heart	heart
38	chr11:34459800-34460600	Active TSS	HepG2	liver
39	chr11:34459800-34460800	Active TSS	Primary T cells fromperipheralblood	blood
40	chr11:34459800-34460800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:34459800-34460800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:34459800-34461000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:34459800-34461000	Active TSS	Primary B cells from peripheral blood	blood
44	chr11:34459800-34461000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:34459800-34461000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:34459800-34461000	Active TSS	Brain Substantia Nigra	brain
47	chr11:34459800-34461000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr11:34459800-34461000	Active TSS	Fetal Brain Male	brain
49	chr11:34459800-34461000	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr11:34459800-34461000	Active TSS	Skeletal Muscle Female	skeletal muscle

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