Variant report

Variant	rs56390038
Chromosome Location	chr11:104828179-104828180
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	MYC	chr11:104828047-104828340	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr11:104828020-104828436	MCF10A-Er-Src	breast:	n/a	chr11:104828185-104828196
3	FOS	chr11:104828125-104828332	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr11:104828111-104828311	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr11:104828035-104828339	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr11:104828111-104828295	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F4	chr11:104828010-104828335	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr11:104828076-104828337	MCF10A-Er-Src	breast:	n/a	chr11:104828185-104828196
9	FOS	chr11:104828113-104828334	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr11:104828047-104828302	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr11:104828023-104828380	Hela-S3	cervix:	n/a	n/a
12	STAT3	chr11:104828029-104828377	MCF10A-Er-Src	breast:	n/a	chr11:104828185-104828196
13	STAT3	chr11:104827987-104828375	MCF10A-Er-Src	breast:	n/a	chr11:104828185-104828196

Variant related genes	Relation type
CASP4	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11606407	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34071659	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56014702	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56026330	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56126979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184015	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123277	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949293	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv898356	chr11:104779195-104838471	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104812800-104829200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:104812800-104831800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:104813800-104837200	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:104814000-104838200	Weak transcription	Fetal Kidney	kidney
5	chr11:104817800-104837000	Weak transcription	Right Ventricle	heart
6	chr11:104821200-104829400	Weak transcription	Pancreas	Pancrea
7	chr11:104821200-104836000	Weak transcription	Gastric	stomach
8	chr11:104821800-104829600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:104821800-104831800	Weak transcription	Fetal Stomach	stomach
10	chr11:104821800-104832000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:104821800-104834400	Weak transcription	Thymus	Thymus
12	chr11:104821800-104836600	Weak transcription	Aorta	Aorta
13	chr11:104821800-104837400	Weak transcription	HSMMtube	muscle
14	chr11:104822000-104834200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:104822000-104836800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:104822200-104831600	Weak transcription	Lung	lung
17	chr11:104822200-104832000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:104824200-104832000	Weak transcription	Spleen	Spleen
19	chr11:104824400-104836000	Weak transcription	Psoas Muscle	Psoas
20	chr11:104825000-104831800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:104825200-104831200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:104825200-104831800	Weak transcription	Ovary	ovary
23	chr11:104825200-104832200	Weak transcription	Osteobl	bone
24	chr11:104825200-104834400	Weak transcription	Fetal Lung	lung
25	chr11:104825400-104831600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:104825400-104832800	Weak transcription	Adipose Nuclei	Adipose
27	chr11:104825400-104836400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:104825400-104836600	Weak transcription	Left Ventricle	heart
29	chr11:104825400-104836800	Weak transcription	Esophagus	oesophagus
30	chr11:104825400-104837400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:104825400-104838200	Weak transcription	HSMM	muscle
32	chr11:104825600-104828400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:104825600-104828600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:104825600-104830600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:104825600-104831000	Weak transcription	Placenta	Placenta
36	chr11:104825600-104831400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:104825600-104831600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:104825600-104831800	Weak transcription	Fetal Intestine Large	intestine
39	chr11:104825600-104832000	Weak transcription	Fetal Muscle Leg	muscle
40	chr11:104825600-104834200	Weak transcription	Fetal Thymus	thymus
41	chr11:104825600-104835800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:104825600-104836800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:104825800-104828200	Weak transcription	GM12878-XiMat	blood
44	chr11:104825800-104829200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:104825800-104829200	Weak transcription	Dnd41	blood
46	chr11:104825800-104831800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:104825800-104832000	Weak transcription	Primary T cells from cord blood	blood
48	chr11:104825800-104832000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:104825800-104832000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:104825800-104835800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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