Variant report

Variant	rs947940
Chromosome Location	chr11:57546564-57546565
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	RCOR1	chr11:57545605-57546585	Hela-S3	cervix:	n/a	n/a
2	ARID3A	chr11:57545507-57546783	HepG2	liver:	n/a	chr11:57546528-57546544 chr11:57546529-57546545
3	NFIC	chr11:57545328-57546625	HepG2	liver:	n/a	chr11:57546157-57546174
4	POLR2A	chr11:57544867-57547756	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZBTB7A	chr11:57545933-57546572	ECC-1	luminal epithelium:	n/a	n/a
6	KAP1	chr11:57545456-57546986	U2OS	brain:	n/a	n/a
7	FOXA1	chr11:57545366-57546585	HepG2	liver:	n/a	n/a
8	RAD21	chr11:57545919-57546589	HepG2	liver:	n/a	n/a
9	EP300	chr11:57545248-57546666	A549	lung:	n/a	chr11:57545349-57545359 chr11:57546229-57546243
10	RFX5	chr11:57546491-57546627	K562	blood:	n/a	n/a
11	MBD4	chr11:57545446-57547182	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:57545258-57547384	HUVEC	blood vessel:	n/a	n/a
13	GATA3	chr11:57545733-57546573	SK-N-SH	brain:	n/a	chr11:57546554-57546564 chr11:57546231-57546241
14	TEAD4	chr11:57545162-57547397	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:57545241-57546627	HUVEC	blood vessel:	n/a	n/a
16	SP1	chr11:57545270-57546598	A549	lung:	n/a	n/a
17	EP300	chr11:57545816-57546565	ECC-1	luminal epithelium:	n/a	chr11:57546229-57546243
18	EP300	chr11:57545331-57547318	A549	lung:	n/a	chr11:57545349-57545359 chr11:57546229-57546243
19	CHD1	chr11:57545377-57547184	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUND	chr11:57545963-57547195	H1-hESC	embryonic stem cell:	n/a	chr11:57547162-57547174 chr11:57546555-57546564
21	BCL3	chr11:57545743-57546822	A549	lung:	n/a	chr11:57546231-57546240 chr11:57546234-57546243
22	BRCA1	chr11:57546083-57546590	H1-hESC	embryonic stem cell:	n/a	n/a
23	NFIC	chr11:57545385-57546664	HepG2	liver:	n/a	chr11:57546157-57546174
24	GATA3	chr11:57545356-57546573	A549	lung:	n/a	chr11:57545422-57545439 chr11:57546554-57546564 chr11:57546231-57546241
25	MBD4	chr11:57545324-57546581	HepG2	liver:	n/a	n/a
26	SP1	chr11:57545326-57546638	HCT-116	colon:	n/a	n/a
27	TBP	chr11:57545634-57546618	Hela-S3	cervix:	n/a	n/a
28	REST	chr11:57545560-57546664	A549	lung:	n/a	chr11:57546091-57546099 chr11:57546308-57546321 chr11:57546093-57546106
29	SP1	chr11:57545189-57546568	A549	lung:	n/a	n/a
30	SMARCC1	chr11:57545465-57547456	Hela-S3	cervix:	n/a	n/a
31	EP300	chr11:57545789-57546688	T-47D	breast:	n/a	chr11:57546229-57546243
32	MAX	chr11:57545386-57546621	A549	lung:	n/a	n/a
33	EP300	chr11:57545256-57546588	HepG2	liver:	n/a	chr11:57545349-57545359 chr11:57546229-57546243
34	POLR2A	chr11:57545283-57547501	HUVEC	blood vessel:	n/a	n/a
35	TBP	chr11:57545415-57547172	HepG2	liver:	n/a	n/a
36	MYBL2	chr11:57545181-57547270	HepG2	liver:	n/a	n/a
37	REST	chr11:57545454-57546807	H1-neurons	neurons:	n/a	chr11:57546091-57546099 chr11:57546308-57546321 chr11:57546093-57546106
38	KAP1	chr11:57545372-57547257	HEK293	kidney:	n/a	n/a
39	TCF12	chr11:57545220-57547313	A549	lung:	n/a	chr11:57546146-57546154
40	POLR2A	chr11:57545759-57546577	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr11:57545452-57546687	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAZ	chr11:57545066-57546835	IMR90	lung:	n/a	n/a
43	POLR2A	chr11:57545073-57547421	HepG2	liver:	n/a	n/a
44	MYBL2	chr11:57545267-57547273	HepG2	liver:	n/a	n/a
45	SP1	chr11:57545435-57546579	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57510237..57513047-chr11:57544366..57548086,3	MCF-7	breast:
2	chr11:57527377..57534826-chr11:57541861..57548775,13	MCF-7	breast:
3	chr11:57517755..57521184-chr11:57545638..57549281,5	MCF-7	breast:
4	chr11:57509911..57512073-chr11:57545879..57548404,2	MCF-7	breast:
5	chr11:57529135..57533999-chr11:57544009..57550841,10	MCF-7	breast:
6	chr11:57422766..57425060-chr11:57546530..57548326,2	MCF-7	breast:
7	chr11:57545694..57547445-chr11:57547779..57550427,3	MCF-7	breast:
8	chr11:57545406..57547871-chr11:57550321..57552770,3	MCF-7	breast:
9	chr11:57540348..57543144-chr11:57545793..57547381,2	K562	blood:
10	chr11:57545030..57547537-chr11:57565376..57568397,5	MCF-7	breast:
11	chr11:57531061..57532831-chr11:57545293..57547269,2	K562	blood:
12	chr11:57545587..57547830-chr11:57553519..57555695,2	MCF-7	breast:
13	chr11:57517889..57520334-chr11:57544692..57547242,2	MCF-7	breast:
14	chr11:57544135..57547056-chr11:57548257..57551353,3	K562	blood:
15	chr11:57532498..57533110-chr11:57545878..57546781,2	MCF-7	breast:
16	chr11:57545891..57547434-chr11:57557245..57559839,2	K562	blood:

Variant related genes	Relation type
CTNND1	TF binding region
ENSG00000198561	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000233436	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10444364	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10736687	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10750868	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10896643	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12284427	0.87[AMR][1000 genomes]
rs1313360	1.00[ASN][1000 genomes]
rs1553827	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1798174	1.00[ASN][1000 genomes]
rs1939322	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2860261	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34430954	1.00[ASN][1000 genomes]
rs474073	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs474464	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs505995	1.00[ASN][1000 genomes]
rs523739	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs529838	1.00[CHB][hapmap]
rs542777	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs552122	1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs554140	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs557051	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786036	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55838210	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56879142	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57201273	1.00[ASN][1000 genomes]
rs57260887	1.00[ASN][1000 genomes]
rs576786	0.91[AFR][1000 genomes]
rs57759830	1.00[ASN][1000 genomes]
rs58176671	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs585190	1.00[ASN][1000 genomes]
rs58851976	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59046396	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60076210	1.00[ASN][1000 genomes]
rs60282001	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60897155	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61444907	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61638601	1.00[ASN][1000 genomes]
rs61743110	1.00[ASN][1000 genomes]
rs627861	1.00[ASN][1000 genomes]
rs635663	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs637116	1.00[ASN][1000 genomes]
rs648412	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103407	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103768	1.00[ASN][1000 genomes]
rs7105331	1.00[ASN][1000 genomes]
rs7110490	1.00[ASN][1000 genomes]
rs7112557	1.00[ASN][1000 genomes]
rs7118249	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7118308	1.00[ASN][1000 genomes]
rs7122105	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7131175	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73472468	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73474417	1.00[ASN][1000 genomes]
rs73474449	1.00[ASN][1000 genomes]
rs73474453	1.00[ASN][1000 genomes]
rs73474454	1.00[ASN][1000 genomes]
rs73474455	1.00[ASN][1000 genomes]
rs73474476	1.00[ASN][1000 genomes]
rs73482748	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482786	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482796	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482801	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7928666	1.00[ASN][1000 genomes]
rs7938752	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	58 gene(s)	inside rSNPs	diseases
7	nsv327	chr11:57532641-57550746	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57538400-57549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:57539600-57552000	Enhancers	Placenta	Placenta
3	chr11:57541600-57550400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr11:57541800-57549000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:57542400-57548800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr11:57542600-57549200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:57542600-57550600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:57542800-57546600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:57543000-57547200	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr11:57543000-57547400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr11:57543000-57547800	Enhancers	Fetal Thymus	thymus
12	chr11:57543000-57551200	Enhancers	Pancreas	Pancrea
13	chr11:57543400-57549000	Enhancers	Primary T cells from cord blood	blood
14	chr11:57543600-57547400	Enhancers	Esophagus	oesophagus
15	chr11:57543800-57548600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr11:57544400-57547200	Enhancers	Fetal Muscle Trunk	muscle
17	chr11:57544400-57550000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr11:57544600-57547000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr11:57544600-57547200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr11:57544600-57547600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr11:57544800-57547000	Enhancers	Thymus	Thymus
22	chr11:57544800-57547200	Enhancers	Dnd41	blood
23	chr11:57544800-57547400	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr11:57545000-57547000	Flanking Active TSS	Liver	Liver
25	chr11:57545000-57547200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:57545000-57547200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr11:57545000-57547200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:57545000-57547200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:57545000-57547400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr11:57545000-57547600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:57545200-57546600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:57545200-57546600	Flanking Active TSS	HMEC	breast
33	chr11:57545200-57546800	Flanking Active TSS	NH-A	brain
34	chr11:57545200-57546800	Flanking Active TSS	Osteobl	bone
35	chr11:57545200-57547200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr11:57545200-57547200	Flanking Active TSS	Hela-S3	cervix
37	chr11:57545200-57547400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:57545200-57547600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:57545200-57551600	Weak transcription	Gastric	stomach
40	chr11:57545200-57555400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:57545400-57546800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:57545400-57546800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr11:57545400-57547200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:57545400-57547200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:57545400-57547200	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr11:57545400-57547200	Flanking Active TSS	NHEK	skin
47	chr11:57545400-57547400	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr11:57545400-57548000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr11:57545600-57546600	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr11:57545600-57546600	Flanking Active TSS	Fetal Muscle Leg	muscle

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