Variant report

Variant	rs9919746
Chromosome Location	chr12:105500422-105500423
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:105499892-105502605	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr12:105500112-105503958	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr12:105500335-105500455	GM12878	blood:	n/a	n/a
4	HCFC1	chr12:105500332-105502938	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr12:105500402-105500435	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr12:105500414-105500787	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105476762..105478986-chr12:105499431..105503042,4	K562	blood:
2	chr12:105379932..105381513-chr12:105500073..105501775,2	MCF-7	breast:
3	chr12:104530239..104532383-chr12:105499797..105502736,2	MCF-7	breast:
4	chr12:104681104..104682731-chr12:105500276..105502937,2	K562	blood:
5	chr12:105499144..105502991-chr12:105627617..105631044,5	MCF-7	breast:
6	chr12:105500023..105502355-chr12:105628064..105629909,2	K562	blood:
7	chr12:105478183..105481313-chr12:105498999..105500811,3	K562	blood:
8	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:
9	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:

No data

Variant related genes	Relation type
KIAA1033	TF binding region
ENSG00000151131	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction
ENSG00000136010	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1014502	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10431460	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1057110	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1077896	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861359	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10861361	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1109433	0.86[EUR][1000 genomes]
rs11112369	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112370	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112372	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112375	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112376	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112379	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112388	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11112409	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112412	0.93[EUR][1000 genomes]
rs11112415	0.89[EUR][1000 genomes]
rs11112416	0.88[EUR][1000 genomes]
rs11112421	0.85[EUR][1000 genomes]
rs11112423	0.84[EUR][1000 genomes]
rs11112432	0.84[EUR][1000 genomes]
rs11831854	0.92[EUR][1000 genomes]
rs11832489	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11834277	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228093	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12228948	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12812433	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12815031	0.88[EUR][1000 genomes]
rs12819309	0.87[EUR][1000 genomes]
rs12830078	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1317955	0.88[EUR][1000 genomes]
rs1373552	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1444611	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1470381	0.87[EUR][1000 genomes]
rs2272495	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293643	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2293644	0.86[EUR][1000 genomes]
rs2464176	0.82[ASN][1000 genomes]
rs28549976	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34075890	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34983773	0.87[EUR][1000 genomes]
rs35462155	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35672903	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3736628	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3794222	0.86[EUR][1000 genomes]
rs3794223	0.87[EUR][1000 genomes]
rs3794224	0.84[EUR][1000 genomes]
rs3794227	0.89[EUR][1000 genomes]
rs3817607	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3829296	0.86[EUR][1000 genomes]
rs4964125	0.88[EUR][1000 genomes]
rs4964334	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964335	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964336	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964338	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964339	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964340	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964342	0.94[EUR][1000 genomes]
rs55908437	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56693261	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73179994	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485364	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs755604	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8015	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs881279	0.88[EUR][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105494800-105500600	Weak transcription	NH-A	brain
2	chr12:105495000-105500600	Weak transcription	NHDF-Ad	bronchial
3	chr12:105495000-105500800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:105500000-105500600	Weak transcription	NHLF	lung
5	chr12:105500200-105500600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr12:105500200-105500600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:105500200-105500600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:105500200-105500600	Enhancers	Colon Smooth Muscle	Colon
9	chr12:105500200-105500600	Bivalent Enhancer	Dnd41	blood
10	chr12:105500200-105500800	Enhancers	Fetal Intestine Small	intestine
11	chr12:105500200-105501000	Flanking Active TSS	NHEK	skin
12	chr12:105500200-105501400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:105500200-105502400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:105500200-105502400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:105500200-105502800	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr12:105500200-105503000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:105500200-105504000	Active TSS	Brain Anterior Caudate	brain
18	chr12:105500400-105500600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:105500400-105500600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr12:105500400-105500600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:105500400-105500600	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr12:105500400-105500600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:105500400-105500600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:105500400-105500600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:105500400-105500600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:105500400-105500600	Enhancers	Adipose Nuclei	Adipose
27	chr12:105500400-105500600	Enhancers	Brain Hippocampus Middle	brain
28	chr12:105500400-105500600	Enhancers	Fetal Intestine Large	intestine
29	chr12:105500400-105500600	Flanking Active TSS	GM12878-XiMat	blood
30	chr12:105500400-105500600	Flanking Active TSS	HepG2	liver
31	chr12:105500400-105500600	Enhancers	Osteobl	bone
32	chr12:105500400-105500800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:105500400-105500800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:105500400-105500800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
35	chr12:105500400-105500800	Flanking Active TSS	Liver	Liver
36	chr12:105500400-105500800	Flanking Active TSS	A549	lung
37	chr12:105500400-105500800	Enhancers	Hela-S3	cervix
38	chr12:105500400-105501000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:105500400-105501000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:105500400-105501000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:105500400-105501000	Flanking Active TSS	HMEC	breast
42	chr12:105500400-105502600	Active TSS	Fetal Brain Female	brain
43	chr12:105500400-105503200	Active TSS	Brain Angular Gyrus	brain
44	chr12:105500400-105503400	Active TSS	Stomach Smooth Muscle	stomach
45	chr12:105500400-105503800	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:105500400-105504600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr12:105500400-105505000	Active TSS	K562	blood

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