Variant report

Variant	rs11174402
Chromosome Location	chr12:62657838-62657839
allele	A/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	TBL1XR1	chr12:62656745-62657843	K562	blood:	n/a	n/a
2	WRNIP1	chr12:62657817-62658149	GM12878	blood:	n/a	n/a
3	MAX	chr12:62657680-62658000	K562	blood:	n/a	n/a
4	EBF1	chr12:62657831-62658031	GM12878	blood:	n/a	chr12:62657851-62657862
5	MAX	chr12:62657750-62657995	K562	blood:	n/a	n/a
6	EGR1	chr12:62657721-62657961	K562	blood:	n/a	n/a
7	MYC	chr12:62657810-62657973	K562	blood:	n/a	n/a
8	POLR2A	chr12:62657796-62657911	MCF-7	breast:	n/a	n/a
9	POLR2A	chr12:62657811-62657923	A549	lung:	n/a	n/a
10	IRF1	chr12:62657524-62659433	K562	blood:	n/a	chr12:62658693-62658707 chr12:62658695-62658706 chr12:62658692-62658706 chr12:62658410-62658420 chr12:62658694-62658708 chr12:62658696-62658710 chr12:62658692-62658712
11	POLR2A	chr12:62657716-62658094	K562	blood:	n/a	n/a
12	BHLHE40	chr12:62657657-62658042	GM12878	blood:	n/a	n/a
13	RCOR1	chr12:62657804-62658028	K562	blood:	n/a	n/a
14	RUNX3	chr12:62657708-62658148	GM12878	blood:	n/a	chr12:62658115-62658124 chr12:62658115-62658124

No.	Distal block	Cell Line	Cell type
1	chr12:62656909..62660165-chr12:62669931..62675800,5	K562	blood:
2	chr12:62655605..62659464-chr12:62666404..62669367,3	MCF-7	breast:
3	chr12:62657511..62660316-chr12:62711919..62713986,2	K562	blood:
4	chr12:62652133..62655871-chr12:62655983..62662487,11	MCF-7	breast:

Variant related genes	Relation type
FAM19A2	TF binding region
ENSG00000135655	Chromatin interaction
ENSG00000198673	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11174406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174407	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174414	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174415	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174429	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174443	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174444	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174454	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174457	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174461	1.00[ASN][1000 genomes]
rs11174462	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174476	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174479	1.00[ASN][1000 genomes]
rs11174492	1.00[ASN][1000 genomes]
rs11174499	1.00[ASN][1000 genomes]
rs11174500	1.00[ASN][1000 genomes]
rs11174501	1.00[ASN][1000 genomes]
rs12811821	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814369	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816968	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818818	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821047	0.88[EUR][1000 genomes]
rs12821894	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826072	0.95[EUR][1000 genomes]
rs17718211	1.00[ASN][1000 genomes]
rs34007988	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34162598	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34251904	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34301355	1.00[ASN][1000 genomes]
rs34339271	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34684698	1.00[ASN][1000 genomes]
rs35360491	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35533759	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71465148	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71465151	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314752	1.00[ASN][1000 genomes]
rs7973386	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978244	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1049465	chr12:62657011-62785005	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62654800-62660600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:62655000-62659400	Weak transcription	Esophagus	oesophagus
3	chr12:62655000-62663400	Weak transcription	Lung	lung
4	chr12:62655200-62658400	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr12:62655400-62658200	Enhancers	Colon Smooth Muscle	Colon
6	chr12:62655400-62660800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:62655400-62685600	Weak transcription	HSMM	muscle
8	chr12:62655600-62661400	Weak transcription	NH-A	brain
9	chr12:62655800-62658400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr12:62655800-62659400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:62655800-62661200	Weak transcription	Osteobl	bone
12	chr12:62656000-62658200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr12:62656000-62658800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:62656000-62660800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:62656000-62661000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:62656000-62661200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:62656000-62661400	Weak transcription	Stomach Mucosa	stomach
18	chr12:62656000-62662000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:62656000-62663200	Weak transcription	Placenta	Placenta
20	chr12:62656000-62664800	Weak transcription	Fetal Stomach	stomach
21	chr12:62656000-62665400	Weak transcription	Brain Angular Gyrus	brain
22	chr12:62656000-62668200	Weak transcription	Right Atrium	heart
23	chr12:62656200-62658000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:62656200-62659800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:62656200-62661000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:62656200-62661200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:62656400-62658000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
28	chr12:62656400-62658200	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr12:62656400-62661200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:62656400-62669600	Enhancers	Liver	Liver
31	chr12:62656400-62679400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:62656600-62658400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:62656600-62658400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:62656600-62659200	Enhancers	Duodenum Mucosa	Duodenum
35	chr12:62656600-62659200	Weak transcription	Small Intestine	intestine
36	chr12:62656600-62659400	Weak transcription	Right Ventricle	heart
37	chr12:62656600-62660800	Weak transcription	NHLF	lung
38	chr12:62656600-62661000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:62656600-62661000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:62656600-62661400	Weak transcription	HMEC	breast
41	chr12:62656600-62661400	Weak transcription	HUVEC	blood vessel
42	chr12:62656600-62662200	Weak transcription	Adipose Nuclei	Adipose
43	chr12:62656600-62663200	Weak transcription	Ovary	ovary
44	chr12:62656600-62664000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:62656600-62668400	Weak transcription	Fetal Brain Female	brain
46	chr12:62656600-62685600	Weak transcription	Aorta	Aorta
47	chr12:62656600-62685600	Weak transcription	Pancreas	Pancrea
48	chr12:62656800-62658200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:62656800-62658800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:62656800-62659000	Enhancers	Primary monocytes fromperipheralblood	blood

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