Variant report

Variant	rs16865452
Chromosome Location	chr2:178484469-178484470
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	HCFC1	chr2:178483122-178484524	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr2:178483011-178484677	SK-N-SH	brain:	n/a	chr2:178483455-178483470 chr2:178483453-178483468

No.	Distal block	Cell Line	Cell type
1	chr2:178255830..178259425-chr2:178483453..178485926,4	K562	blood:
2	chr2:178076328..178078766-chr2:178482248..178484815,2	K562	blood:
3	chr2:178416378..178418708-chr2:178482397..178484777,2	MCF-7	breast:

Variant related genes	Relation type
TTC30A	TF binding region
ENSG00000196659	Chromatin interaction
ENSG00000213963	Chromatin interaction
ENSG00000229337	Chromatin interaction
ENSG00000170144	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000018510	Chromatin interaction
ENSG00000263721	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10497494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497495	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10497498	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1106074	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1527405	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1527408	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs16865443	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs16865444	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs16865446	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs16865448	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs16865449	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs16865453	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16865475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16865492	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16865501	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16865508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16865509	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16865514	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16865524	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2178018	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2293472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2365618	0.92[ASN][1000 genomes]
rs2695317	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs3731803	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731804	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3731806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770018	0.82[JPT][hapmap]
rs3813256	0.86[ASN][1000 genomes]
rs3821003	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821004	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4144277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025339	0.92[ASN][1000 genomes]
rs57000468	0.83[ASN][1000 genomes]
rs57401542	0.83[ASN][1000 genomes]
rs57479066	0.85[ASN][1000 genomes]
rs58970701	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59275027	0.85[ASN][1000 genomes]
rs59677452	0.85[ASN][1000 genomes]
rs59963196	0.92[ASN][1000 genomes]
rs60941291	0.83[ASN][1000 genomes]
rs61164370	0.81[ASN][1000 genomes]
rs61311927	0.81[ASN][1000 genomes]
rs61425825	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61457959	0.92[ASN][1000 genomes]
rs61570618	0.92[ASN][1000 genomes]
rs6745743	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6746845	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs73977682	0.85[ASN][1000 genomes]
rs73977683	0.85[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178484000-178487400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:178484000-178499200	Weak transcription	Pancreas	Pancrea
3	chr2:178484200-178484600	Enhancers	Fetal Brain Female	brain
4	chr2:178484200-178484800	Enhancers	Fetal Lung	lung
5	chr2:178484200-178487000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:178484200-178487200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:178484200-178487200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:178484200-178487200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:178484200-178487400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:178484200-178487400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:178484200-178487400	Weak transcription	Psoas Muscle	Psoas
12	chr2:178484200-178487600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:178484200-178487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:178484200-178487600	Weak transcription	HUVEC	blood vessel
15	chr2:178484200-178490600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:178484200-178490600	Weak transcription	Fetal Stomach	stomach
17	chr2:178484200-178490800	Weak transcription	Right Atrium	heart
18	chr2:178484400-178485400	Enhancers	HepG2	liver
19	chr2:178484400-178485600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:178484400-178486800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:178484400-178487000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:178484400-178487000	Weak transcription	Fetal Kidney	kidney
23	chr2:178484400-178487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:178484400-178487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:178484400-178487200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:178484400-178487200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:178484400-178487200	Weak transcription	Brain Anterior Caudate	brain
28	chr2:178484400-178487200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:178484400-178487400	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:178484400-178487400	Weak transcription	Fetal Brain Male	brain
31	chr2:178484400-178487400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:178484400-178487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:178484400-178487600	Weak transcription	Liver	Liver
34	chr2:178484400-178490400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:178484400-178490600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:178484400-178490800	Weak transcription	Adipose Nuclei	Adipose
37	chr2:178484400-178490800	Weak transcription	Colon Smooth Muscle	Colon

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