Variant report

Variant	rs11688877
Chromosome Location	chr2:100724445-100724446
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	GATA3	chr2:100724251-100724542	SH-SY5Y	brain:	n/a	chr2:100724477-100724494

Variant related genes	Relation type
AFF3	TF binding region

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11675333	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11680846	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11684692	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11685258	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11685397	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11691359	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11692695	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693242	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11693804	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11695782	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12998219	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13019124	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17352731	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17437470	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1821831	0.85[EUR][1000 genomes]
rs34754366	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34851723	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35167301	0.82[EUR][1000 genomes]
rs35462405	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35720347	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35742951	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6724583	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6736637	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6738012	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6740622	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6748064	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74177693	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7594938	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv458707	chr2:100687778-100753490	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv582529	chr2:100687778-100753490	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1793611	chr2:100693049-100725966	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv2847	chr2:100695863-100726149	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100722000-100725200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:100722000-100729400	Weak transcription	Dnd41	blood
3	chr2:100722200-100726200	Genic enhancers	Primary B cells from cord blood	blood
4	chr2:100722200-100726800	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr2:100722200-100727600	Weak transcription	Primary T cells from cord blood	blood
6	chr2:100722400-100726200	Weak transcription	Thymus	Thymus
7	chr2:100722400-100726400	Weak transcription	Spleen	Spleen
8	chr2:100722400-100726600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:100722400-100726600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:100722400-100730000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:100722600-100724600	Enhancers	Colon Smooth Muscle	Colon
12	chr2:100722600-100725400	Enhancers	Fetal Kidney	kidney
13	chr2:100722600-100726000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:100722600-100726000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:100722600-100726200	Weak transcription	Fetal Thymus	thymus
16	chr2:100722800-100724600	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:100722800-100725400	Enhancers	Fetal Brain Male	brain
18	chr2:100723000-100727000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:100723200-100724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:100723400-100724600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:100723400-100724800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:100723400-100724800	Weak transcription	Brain Germinal Matrix	brain
23	chr2:100724000-100725000	Bivalent Enhancer	Fetal Stomach	stomach
24	chr2:100724000-100725200	Enhancers	Fetal Brain Female	brain
25	chr2:100724000-100725200	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr2:100724000-100725200	Enhancers	Ovary	ovary
27	chr2:100724200-100725200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:100724200-100725200	Enhancers	Brain Angular Gyrus	brain
29	chr2:100724400-100724600	Enhancers	Gastric	stomach
30	chr2:100724400-100724600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
31	chr2:100724400-100725200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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