Variant report

Variant	rs11888876
Chromosome Location	chr2:97477842-97477843
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	CEBPB	chr2:97477677-97478167	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:97477800-97477905	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:97477623-97477914	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:97477747-97477936	MCF10A-Er-Src	breast:	n/a	chr2:97477854-97477861

Variant related genes	Relation type
CNNM3	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1108786	1.00[EUR][1000 genomes]
rs11890388	1.00[EUR][1000 genomes]
rs11902657	1.00[EUR][1000 genomes]
rs17119533	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs35069910	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3806559	1.00[EUR][1000 genomes]
rs57537489	1.00[EUR][1000 genomes]
rs58225390	1.00[EUR][1000 genomes]
rs6576982	1.00[EUR][1000 genomes]
rs6729813	1.00[EUR][1000 genomes]
rs72939374	1.00[EUR][1000 genomes]
rs72939397	1.00[EUR][1000 genomes]
rs72941206	1.00[EUR][1000 genomes]
rs72941231	1.00[EUR][1000 genomes]
rs72942920	1.00[EUR][1000 genomes]
rs72942941	1.00[EUR][1000 genomes]
rs72942947	1.00[EUR][1000 genomes]
rs73959007	1.00[EUR][1000 genomes]
rs73959410	1.00[EUR][1000 genomes]
rs73959411	1.00[EUR][1000 genomes]
rs7575530	1.00[EUR][1000 genomes]
rs7583821	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	55 gene(s)	inside rSNPs	diseases
11	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
12	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97440000-97480800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:97454600-97481000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:97454600-97481000	Weak transcription	NHEK	skin
4	chr2:97455400-97480600	Weak transcription	Hela-S3	cervix
5	chr2:97462000-97480800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:97464600-97480800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:97465200-97481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:97465400-97481200	Weak transcription	Small Intestine	intestine
9	chr2:97466000-97481200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:97466800-97478000	Weak transcription	NHLF	lung
11	chr2:97466800-97478600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:97466800-97480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:97466800-97481000	Weak transcription	HMEC	breast
14	chr2:97467800-97481000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:97467800-97481000	Weak transcription	Fetal Brain Male	brain
16	chr2:97468000-97480800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:97468000-97480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:97468000-97481000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:97468400-97480800	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:97472400-97478400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:97472800-97478000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr2:97472800-97478400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:97473000-97479600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:97473000-97481000	Weak transcription	Primary B cells from cord blood	blood
25	chr2:97473200-97480800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:97473200-97480800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:97473600-97481000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:97473800-97481000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:97474000-97480800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:97474200-97478600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:97474200-97479400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:97474200-97479400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:97474200-97480800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:97474200-97480800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:97474200-97480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:97474200-97481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:97474400-97479200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:97474400-97480800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:97474600-97481000	Weak transcription	Ovary	ovary
40	chr2:97474800-97478000	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr2:97475000-97478200	Strong transcription	GM12878-XiMat	blood
42	chr2:97475000-97479600	Enhancers	Fetal Heart	heart
43	chr2:97475200-97478600	Enhancers	HSMM	muscle
44	chr2:97475200-97481000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:97475400-97478400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:97475400-97478600	Enhancers	Right Ventricle	heart
47	chr2:97475400-97480800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:97475400-97481000	Weak transcription	Aorta	Aorta
49	chr2:97475600-97478800	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr2:97475800-97478800	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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