Variant report

Variant	rs787175
Chromosome Location	chr2:144712417-144712418
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	chr2:144712357-144713580	SK-N-SH	brain:	n/a	chr2:144713358-144713367 chr2:144712650-144712657 chr2:144713358-144713368
2	GATA3	chr2:144712288-144713708	SK-N-SH	brain:	n/a	chr2:144713358-144713367 chr2:144712650-144712657 chr2:144713358-144713368
3	TEAD4	chr2:144712341-144713598	SK-N-SH	brain:	n/a	chr2:144712996-144713005
4	EP300	chr2:144712375-144712780	SK-N-SH_RA	brain:	n/a	n/a
5	TCF12	chr2:144712393-144713755	SK-N-SH	brain:	n/a	chr2:144713466-144713473
6	EP300	chr2:144711581-144713862	SK-N-SH	brain:	n/a	chr2:144713485-144713499

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:144711849..144715713-chr2:144717627..144720875,3	K562	blood:

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10185661	0.92[ASW][hapmap];0.87[GIH][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10496956	0.84[MEX][hapmap]
rs1257048	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13402935	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs35304150	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription 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 target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer 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 target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs787175	GTDC1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144695400-144714200	Weak transcription	Gastric	stomach
2	chr2:144696000-144713200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:144696600-144712600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:144696600-144717800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:144699600-144730400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:144700800-144719600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:144704400-144713400	Weak transcription	Esophagus	oesophagus
8	chr2:144704600-144713400	Weak transcription	Lung	lung
9	chr2:144704600-144728800	Weak transcription	Spleen	Spleen
10	chr2:144704800-144712600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:144704800-144712600	Weak transcription	Fetal Stomach	stomach
12	chr2:144704800-144713200	Weak transcription	Liver	Liver
13	chr2:144704800-144719200	Weak transcription	Primary B cells from cord blood	blood
14	chr2:144704800-144730800	Weak transcription	Left Ventricle	heart
15	chr2:144705000-144717800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:144707200-144712600	Weak transcription	Fetal Heart	heart
17	chr2:144707200-144713200	Enhancers	Fetal Brain Male	brain
18	chr2:144708000-144713000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:144709200-144714600	Weak transcription	Fetal Kidney	kidney
20	chr2:144710800-144713600	Enhancers	Osteobl	bone
21	chr2:144711000-144713400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:144711000-144713600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:144711000-144713800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:144711200-144713800	Enhancers	HSMM	muscle
25	chr2:144711400-144712800	Enhancers	NHDF-Ad	bronchial
26	chr2:144711400-144713000	Weak transcription	Fetal Brain Female	brain
27	chr2:144711400-144713200	Enhancers	Fetal Lung	lung
28	chr2:144711400-144713600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:144711400-144713800	Enhancers	NHLF	lung
30	chr2:144711400-144717600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:144711600-144713200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:144711800-144713000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:144711800-144713200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:144711800-144713200	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:144711800-144713400	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:144711800-144714800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:144712000-144713200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:144712000-144713200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:144712000-144713200	Weak transcription	Ovary	ovary
40	chr2:144712000-144713800	Enhancers	NH-A	brain
41	chr2:144712000-144715200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr2:144712200-144713600	Enhancers	HSMMtube	muscle
43	chr2:144712400-144713800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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