Variant report

Variant	rs2969942
Chromosome Location	chr11:57477159-57477160
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	POLR2A	chr11:57477149-57477353	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57416825..57418474-chr11:57477020..57479617,2	K562	blood:
2	chr11:57473781..57477362-chr11:57478566..57481637,6	K562	blood:
3	chr11:57433212..57437810-chr11:57477098..57481918,8	MCF-7	breast:
4	chr11:57459870..57462694-chr11:57476257..57478537,2	MCF-7	breast:

Variant related genes	Relation type
TMX2-CTNND1	TF binding region
TMX2	TF binding region
ENSG00000156599	Chromatin interaction
ENSG00000213593	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000254462	Chromatin interaction
ENSG00000156603	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10160797	1.00[AMR][1000 genomes]
rs12282980	1.00[AMR][1000 genomes]
rs1941721	0.85[AFR][1000 genomes]
rs2911725	0.95[AFR][1000 genomes]
rs2926660	0.85[AFR][1000 genomes]
rs2926663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956980	0.95[AFR][1000 genomes]
rs2956983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956984	0.86[AFR][1000 genomes]
rs2969941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2969945	0.85[AFR][1000 genomes]
rs3016261	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016264	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs600251	0.85[AFR][1000 genomes]
rs603420	0.85[AFR][1000 genomes]
rs610801	0.85[AFR][1000 genomes]
rs621683	0.80[AFR][1000 genomes]
rs621731	0.80[AFR][1000 genomes]
rs635536	0.80[AFR][1000 genomes]
rs660400	0.85[AFR][1000 genomes]
rs682785	0.80[AFR][1000 genomes]
rs7127878	1.00[AMR][1000 genomes]
rs7939745	1.00[AMR][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	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv975360	chr11:57466716-57480320	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57436600-57479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57438600-57478200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:57439000-57477400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:57461400-57478400	Weak transcription	Fetal Heart	heart
5	chr11:57464400-57478800	Weak transcription	Psoas Muscle	Psoas
6	chr11:57467600-57478200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:57468400-57478400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:57468400-57478800	Weak transcription	Right Ventricle	heart
9	chr11:57469200-57478800	Weak transcription	Ovary	ovary
10	chr11:57469400-57478800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:57471400-57478000	Weak transcription	Primary B cells from cord blood	blood
12	chr11:57471800-57478400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:57472000-57477800	Weak transcription	K562	blood
14	chr11:57472000-57478400	Weak transcription	Fetal Kidney	kidney
15	chr11:57472000-57478600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:57472000-57478600	Weak transcription	Small Intestine	intestine
17	chr11:57472200-57477400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:57472200-57478400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:57472200-57478400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:57472400-57477600	Weak transcription	HUVEC	blood vessel
21	chr11:57472400-57478000	Weak transcription	Hela-S3	cervix
22	chr11:57472400-57478400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:57472400-57478400	Weak transcription	Brain Angular Gyrus	brain
24	chr11:57472600-57477400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:57472600-57477400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:57472600-57477400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:57472600-57477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:57472600-57477600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:57472600-57477600	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:57472600-57477600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:57472600-57477600	Weak transcription	Lung	lung
32	chr11:57472600-57477600	Weak transcription	Pancreas	Pancrea
33	chr11:57472600-57477600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:57472600-57477600	Weak transcription	NHDF-Ad	bronchial
35	chr11:57472600-57478000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:57472600-57478000	Weak transcription	HSMM	muscle
37	chr11:57472600-57478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:57472600-57478200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr11:57472600-57478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:57472600-57478200	Weak transcription	Gastric	stomach
41	chr11:57472600-57478400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:57472600-57478400	Weak transcription	Brain Substantia Nigra	brain
43	chr11:57472600-57478400	Weak transcription	NHEK	skin
44	chr11:57472600-57478600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr11:57472600-57478600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:57472600-57478600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:57472600-57478600	Weak transcription	NH-A	brain
48	chr11:57472600-57478800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:57472600-57478800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:57472600-57478800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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