Variant report

Variant	rs12080111
Chromosome Location	chr1:246954925-246954926
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	POLR2A	chr1:246952019-246955465	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246951287..246953566-chr1:246953954..246955878,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCCPDH-1	chr1:246953748-246955687	ENSG00000227953.2

Variant related genes	Relation type
KIF28P	TF binding region
ENSG00000227953	Chromatin interaction
ENSG00000223519	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12049149	0.83[ASN][1000 genomes]
rs12058428	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3795462	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4244628	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4926441	0.81[AMR][1000 genomes]
rs4926448	0.81[ASN][1000 genomes]
rs4926453	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60779884	0.98[ASN][1000 genomes]
rs6426332	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6426334	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7513803	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7537149	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7549965	0.80[ASN][1000 genomes]
rs7556120	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats 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	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv525154	chr1:246954166-246963019	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:246945800-246956400	Weak transcription	A549	lung
3	chr1:246946200-246956800	Weak transcription	Left Ventricle	heart
4	chr1:246949000-246957600	Weak transcription	NHDF-Ad	bronchial
5	chr1:246949400-246956800	Weak transcription	Hela-S3	cervix
6	chr1:246949400-246957600	Weak transcription	NHLF	lung
7	chr1:246952600-246956000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:246952600-246956800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:246952600-246957600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:246952600-246957800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:246952800-246956600	Weak transcription	Placenta	Placenta
12	chr1:246952800-246956800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:246952800-246957000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:246952800-246957000	Weak transcription	Brain Germinal Matrix	brain
15	chr1:246952800-246957600	Weak transcription	Fetal Brain Female	brain
16	chr1:246952800-246957800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:246953000-246956800	Weak transcription	Fetal Brain Male	brain
18	chr1:246953000-246957600	Weak transcription	Fetal Heart	heart
19	chr1:246953000-246957600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:246953000-246957600	Weak transcription	Right Ventricle	heart
21	chr1:246953000-246957800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:246953200-246956800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:246953200-246957600	Weak transcription	Spleen	Spleen
24	chr1:246953400-246955400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:246953400-246956200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:246953400-246956400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:246953400-246956400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:246953400-246956400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:246953400-246956400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:246953400-246956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:246953400-246956600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:246953400-246956800	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:246953400-246957000	Weak transcription	Gastric	stomach
34	chr1:246953400-246957600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:246953400-246957600	Weak transcription	Fetal Lung	lung
36	chr1:246953400-246957600	Weak transcription	Ovary	ovary
37	chr1:246953400-246958000	Weak transcription	Fetal Kidney	kidney
38	chr1:246953400-246961600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:246953600-246955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:246953600-246956800	Weak transcription	Fetal Stomach	stomach
41	chr1:246954000-246956200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:246954600-246956000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:246954800-246957600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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