Variant report

Variant	rs55634858
Chromosome Location	chr11:104839645-104839646
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	TBP	chr11:104839106-104840551	HepG2	liver:	n/a	n/a
2	ELF1	chr11:104839017-104839686	HCT-116	colon:	n/a	n/a
3	MAFK	chr11:104839223-104840096	HepG2	liver:	n/a	chr11:104839410-104839426
4	MYBL2	chr11:104839002-104839883	HepG2	liver:	n/a	n/a
5	FOS	chr11:104839099-104839650	MCF10A-Er-Src	breast:	n/a	chr11:104839157-104839166
6	POLR2A	chr11:104838965-104840618	HepG2	liver:	n/a	n/a
7	STAT3	chr11:104838210-104839862	MCF10A-Er-Src	breast:	n/a	chr11:104839303-104839314
8	TCF12	chr11:104838724-104839671	SK-N-SH	brain:	n/a	n/a
9	ELF1	chr11:104838960-104839720	HCT-116	colon:	n/a	n/a
10	SMC3	chr11:104839263-104839810	HepG2	liver:	n/a	n/a
11	GTF2F1	chr11:104839089-104839826	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr11:104837727-104839837	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr11:104838854-104839805	MCF10A-Er-Src	breast:	n/a	chr11:104839303-104839314
14	GATA2	chr11:104838056-104839690	HUVEC	blood vessel:	n/a	chr11:104839653-104839669 chr11:104838280-104838289 chr11:104838840-104838856 chr11:104839650-104839660 chr11:104838842-104838856 chr11:104839653-104839669 chr11:104838843-104838852 chr11:104839651-104839672 chr11:104839157-104839167 chr11:104838279-104838291 chr11:104838277-104838293 chr11:104838280-104838290
15	CHD2	chr11:104839036-104839684	Hela-S3	cervix:	n/a	n/a
16	MAFF	chr11:104839117-104840103	HepG2	liver:	n/a	n/a
17	MAFK	chr11:104839156-104840093	IMR90	lung:	n/a	chr11:104839410-104839426
18	POLR2A	chr11:104837254-104840012	Hela-S3	cervix:	n/a	n/a
19	ELF1	chr11:104839041-104839648	MCF-7	breast:	n/a	n/a
20	HEY1	chr11:104839034-104840602	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:104839605-104840593	HepG2	liver:	n/a	n/a
22	CEBPB	chr11:104838916-104839753	HCT-116	colon:	n/a	n/a
23	POLR2A	chr11:104838348-104840057	HUVEC	blood vessel:	n/a	n/a
24	STAT3	chr11:104838281-104839806	MCF10A-Er-Src	breast:	n/a	chr11:104839303-104839314

Variant related genes	Relation type
CASP4	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1801319	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45504692	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45530635	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45569135	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651735	0.94[EUR][1000 genomes]
rs55721600	0.94[EUR][1000 genomes]
rs55725142	0.94[EUR][1000 genomes]
rs55781362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932228	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56011093	0.94[EUR][1000 genomes]
rs56043157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349036	0.94[EUR][1000 genomes]
rs57760571	0.94[EUR][1000 genomes]
rs59367529	0.94[EUR][1000 genomes]
rs59580775	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59769457	0.94[EUR][1000 genomes]
rs7104993	0.94[EUR][1000 genomes]
rs7116603	0.94[EUR][1000 genomes]
rs7131099	0.94[EUR][1000 genomes]
rs72978960	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978981	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978997	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978998	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7941702	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv832255	chr11:104674918-104846961	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv898355	chr11:104730322-104897843	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1040784	chr11:104763797-104855878	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv1041081	chr11:104797775-104912458	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104836600-104840400	Active TSS	Rectal Smooth Muscle	rectum
2	chr11:104836800-104840200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:104837000-104840000	Active TSS	Right Ventricle	heart
4	chr11:104837000-104840600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr11:104837200-104839800	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr11:104837200-104840200	Active TSS	Psoas Muscle	Psoas
7	chr11:104837400-104839800	Active TSS	NHLF	lung
8	chr11:104837400-104840400	Active TSS	Right Atrium	heart
9	chr11:104837400-104840600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr11:104837600-104839800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:104837600-104839800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:104837600-104839800	Active TSS	Thymus	Thymus
13	chr11:104837600-104840000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:104837600-104840000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:104837600-104840000	Active TSS	Placenta	Placenta
16	chr11:104837600-104840000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:104837800-104839800	Active TSS	NHDF-Ad	bronchial
18	chr11:104837800-104840000	Active TSS	Brain Hippocampus Middle	brain
19	chr11:104837800-104840200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:104837800-104840200	Active TSS	Brain Anterior Caudate	brain
21	chr11:104837800-104840200	Active TSS	Ovary	ovary
22	chr11:104838000-104839800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:104838000-104840200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:104838000-104840400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:104838000-104840600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr11:104838200-104839800	Active TSS	Colonic Mucosa	Colon
27	chr11:104838200-104839800	Active TSS	Fetal Muscle Trunk	muscle
28	chr11:104838200-104839800	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr11:104838200-104840000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr11:104838200-104840000	Active TSS	Fetal Kidney	kidney
31	chr11:104838200-104840200	Active TSS	Aorta	Aorta
32	chr11:104838200-104840200	Active TSS	Left Ventricle	heart
33	chr11:104838200-104840400	Active TSS	HSMM	muscle
34	chr11:104838200-104840400	Active TSS	Osteobl	bone
35	chr11:104838200-104840600	Active TSS	Stomach Smooth Muscle	stomach
36	chr11:104838400-104839800	Active TSS	Muscle Satellite Cultured Cells	--
37	chr11:104838400-104839800	Active TSS	Adipose Nuclei	Adipose
38	chr11:104838400-104839800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr11:104838400-104839800	Active TSS	Fetal Stomach	stomach
40	chr11:104838400-104839800	Active TSS	Lung	lung
41	chr11:104838400-104839800	Active TSS	NH-A	brain
42	chr11:104838400-104840000	Active TSS	Brain Cingulate Gyrus	brain
43	chr11:104838400-104840000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:104838400-104840000	Active TSS	Esophagus	oesophagus
45	chr11:104838400-104840000	Active TSS	Pancreas	Pancrea
46	chr11:104838400-104840400	Active TSS	Colon Smooth Muscle	Colon
47	chr11:104838600-104839800	Active TSS	Fetal Lung	lung
48	chr11:104838600-104840000	Active TSS	Brain Angular Gyrus	brain
49	chr11:104838800-104840200	Active TSS	HSMMtube	muscle
50	chr11:104839000-104839800	Active TSS	Brain Substantia Nigra	brain

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