Variant report

Variant	rs1671688
Chromosome Location	chr12:123255733-123255734
allele	A/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	chr12:123255725-123255774	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123255642-123255847	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123255502..123257176-chr12:123324408..123327320,2	MCF-7	breast:
2	chr12:123237378..123239176-chr12:123253699..123256026,3	MCF-7	breast:
3	chr12:123242966..123245804-chr12:123255360..123258267,2	MCF-7	breast:

Variant related genes	Relation type
CCDC62	TF binding region
ENSG00000139726	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10466883	0.92[ASN][1000 genomes]
rs10466884	0.92[ASN][1000 genomes]
rs11059711	0.92[ASN][1000 genomes]
rs11059724	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11059834	0.94[ASN][1000 genomes]
rs11059932	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11059953	0.91[ASN][1000 genomes]
rs11059954	0.92[ASN][1000 genomes]
rs12302287	0.94[ASN][1000 genomes]
rs12303150	0.92[ASN][1000 genomes]
rs12303270	0.94[ASN][1000 genomes]
rs12303951	0.91[ASN][1000 genomes]
rs12305822	0.91[ASN][1000 genomes]
rs12307038	0.94[ASN][1000 genomes]
rs12310386	0.92[ASN][1000 genomes]
rs12310901	0.94[ASN][1000 genomes]
rs12312837	0.94[ASN][1000 genomes]
rs12316263	0.92[ASN][1000 genomes]
rs12319160	0.91[ASN][1000 genomes]
rs12321100	0.90[ASN][1000 genomes]
rs12321556	0.92[ASN][1000 genomes]
rs1260120	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671679	0.92[ASN][1000 genomes]
rs1696320	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253504	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649902	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936730	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817095	0.92[ASN][1000 genomes]
rs57366988	0.92[ASN][1000 genomes]
rs60469279	0.92[ASN][1000 genomes]
rs61176973	0.94[ASN][1000 genomes]
rs6489240	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652533	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs701484	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7138436	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7311386	0.92[ASN][1000 genomes]
rs7486414	0.92[ASN][1000 genomes]
rs7966971	0.91[ASN][1000 genomes]
rs839363	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9645762	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv975535	chr12:123253274-123256041	Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123238400-123258000	Strong transcription	Fetal Muscle Trunk	muscle
2	chr12:123238600-123255800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr12:123238600-123258800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:123238800-123255800	Strong transcription	Primary B cells from cord blood	blood
5	chr12:123238800-123255800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:123238800-123255800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:123238800-123255800	Strong transcription	Liver	Liver
8	chr12:123238800-123256000	Strong transcription	NH-A	brain
9	chr12:123238800-123256200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:123238800-123256200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:123238800-123256200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:123238800-123256200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:123238800-123256600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:123238800-123257400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:123238800-123257400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:123238800-123257600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:123238800-123257800	Strong transcription	Fetal Thymus	thymus
18	chr12:123238800-123257800	Strong transcription	Osteobl	bone
19	chr12:123238800-123258000	Strong transcription	Placenta	Placenta
20	chr12:123239000-123256600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:123239000-123257400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:123239000-123257600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:123239200-123255800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:123239200-123255800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr12:123239200-123255800	Strong transcription	Adipose Nuclei	Adipose
26	chr12:123239200-123257000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:123239200-123257400	Strong transcription	A549	lung
28	chr12:123239200-123257800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:123239400-123256800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:123239400-123257800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:123239400-123258000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:123239600-123258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:123239800-123256200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:123239800-123257800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:123240400-123257800	Strong transcription	Fetal Brain Female	brain
36	chr12:123241400-123257600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:123241800-123256200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:123242000-123257800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:123242000-123258600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:123242400-123258600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:123243800-123258600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:123244800-123258800	Strong transcription	Dnd41	blood
43	chr12:123245800-123257600	Strong transcription	HSMM	muscle
44	chr12:123246200-123256200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:123247200-123256000	Strong transcription	NHLF	lung
46	chr12:123247400-123258000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:123247800-123257800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:123247800-123258600	Weak transcription	Right Atrium	heart
49	chr12:123248400-123255800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:123248400-123256200	Strong transcription	Primary T cells from cord blood	blood

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