Variant report

Variant	rs10846491
Chromosome Location	chr12:123753492-123753493
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr12:123753376-123754238	GM12878	blood:	n/a	chr12:123753947-123753959
2	POLR2A	chr12:123753036-123754222	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr12:123751836-123757238	SK-N-SH	brain:	n/a	chr12:123755352-123755361
4	POLR2A	chr12:123753070-123754228	H1-hESC	embryonic stem cell:	n/a	n/a
5	RUNX3	chr12:123753065-123753782	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:123753177-123753747	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:123753022-123753603	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:123752762-123757235	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:123753442-123753529	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:123752165-123757291	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:123753412-123753578	ProgFib	skin:	n/a	n/a
12	POLR2A	chr12:123753211-123753789	H1-hESC	embryonic stem cell:	n/a	n/a
13	MTA3	chr12:123752878-123754285	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123717014..123719935-chr12:123753310..123757333,7	K562	blood:
2	chr12:123753478..123757222-chr12:123871925..123875006,5	K562	blood:
3	chr12:123753349..123756927-chr12:123873006..123875020,4	MCF-7	breast:
4	chr12:123753293..123755952-chr12:123766285..123768150,2	MCF-7	breast:
5	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:
6	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
7	chr12:123752887..123754431-chr12:123868251..123870818,2	K562	blood:
8	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:

No data

Variant related genes	Relation type
CDK2AP1	TF binding region
ENSG00000188026	Chromatin interaction
ENSG00000199845	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10732573	0.82[EUR][1000 genomes]
rs10734901	0.82[EUR][1000 genomes]
rs10744149	0.84[AMR][1000 genomes]
rs10772995	0.83[AMR][1000 genomes]
rs10772998	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10773001	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10773002	0.82[EUR][1000 genomes]
rs10846478	0.84[AMR][1000 genomes]
rs10846486	0.84[AMR][1000 genomes]
rs10846487	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11057192	0.85[AMR][1000 genomes]
rs11057204	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057206	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057210	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12817892	0.85[EUR][1000 genomes]
rs12818067	0.85[EUR][1000 genomes]
rs12824957	0.96[EUR][1000 genomes]
rs12829456	0.85[EUR][1000 genomes]
rs1402274	0.82[AMR][1000 genomes]
rs1402275	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1533703	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1615694	0.84[AMR][1000 genomes]
rs1626899	0.88[AMR][1000 genomes]
rs1630693	0.87[AMR][1000 genomes]
rs1630905	0.88[AMR][1000 genomes]
rs1716156	0.81[AMR][1000 genomes]
rs1716157	0.84[AMR][1000 genomes]
rs1716159	0.83[AMR][1000 genomes]
rs1716160	0.88[AMR][1000 genomes]
rs1716164	0.83[AMR][1000 genomes]
rs1716170	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716171	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716172	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716173	0.83[AMR][1000 genomes]
rs1716175	0.83[AMR][1000 genomes]
rs1716176	0.82[AMR][1000 genomes]
rs1716177	0.82[AMR][1000 genomes]
rs1716182	0.82[AMR][1000 genomes]
rs1727290	0.82[AMR][1000 genomes]
rs1727300	0.83[AMR][1000 genomes]
rs1727306	0.83[AMR][1000 genomes]
rs1727320	0.88[AMR][1000 genomes]
rs1727323	0.85[AMR][1000 genomes]
rs1727325	0.84[AMR][1000 genomes]
rs1727334	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1790086	0.84[AMR][1000 genomes]
rs1790087	0.84[AMR][1000 genomes]
rs1790089	0.82[AMR][1000 genomes]
rs1790095	0.82[AMR][1000 genomes]
rs1790098	0.82[AMR][1000 genomes]
rs1790100	0.82[AMR][1000 genomes]
rs1790101	0.88[AMR][1000 genomes]
rs1790102	0.87[AMR][1000 genomes]
rs1790124	0.83[AMR][1000 genomes]
rs1790125	0.80[AMR][1000 genomes]
rs1790130	0.88[AMR][1000 genomes]
rs1790131	0.88[AMR][1000 genomes]
rs1879380	0.93[EUR][1000 genomes]
rs1969354	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1980251	0.82[EUR][1000 genomes]
rs1980252	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2049114	0.83[AMR][1000 genomes]
rs2337934	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2682430	0.88[AMR][1000 genomes]
rs2682431	0.88[AMR][1000 genomes]
rs2682434	0.85[AMR][1000 genomes]
rs2851436	0.83[AMR][1000 genomes]
rs2851450	0.86[AMR][1000 genomes]
rs2851451	0.84[AMR][1000 genomes]
rs2950537	0.82[AMR][1000 genomes]
rs3018098	0.82[AMR][1000 genomes]
rs34341465	0.85[EUR][1000 genomes]
rs4268544	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4372492	0.85[AMR][1000 genomes]
rs4759371	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759409	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759415	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759416	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759417	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58809476	0.85[EUR][1000 genomes]
rs6633	0.95[EUR][1000 genomes]
rs7313483	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7953929	0.92[EUR][1000 genomes]
rs941305	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs941306	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9795522	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats 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	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10846491	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs10846491	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10846491	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs10846491	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10846491	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10846491	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10846491	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123739200-123754200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:123740000-123753600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:123741000-123753600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:123742400-123754600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:123742400-123754600	Weak transcription	Small Intestine	intestine
6	chr12:123743000-123754200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:123743400-123754000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:123743600-123753600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:123744000-123753800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:123744000-123753800	Weak transcription	K562	blood
11	chr12:123745400-123754000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:123746600-123754000	Weak transcription	Fetal Kidney	kidney
13	chr12:123747000-123754400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:123749200-123753800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:123749400-123754600	Enhancers	Fetal Brain Male	brain
16	chr12:123750400-123753800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:123750600-123753800	Weak transcription	Hela-S3	cervix
18	chr12:123751000-123753800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:123751400-123753800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:123751400-123753800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:123751400-123753800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:123751800-123753600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:123751800-123753600	Weak transcription	Fetal Intestine Large	intestine
24	chr12:123751800-123753600	Genic enhancers	Fetal Stomach	stomach
25	chr12:123751800-123754200	Weak transcription	Aorta	Aorta
26	chr12:123751800-123754200	Flanking Active TSS	HSMMtube	muscle
27	chr12:123752000-123754000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:123752000-123754000	Flanking Active TSS	Fetal Brain Female	brain
29	chr12:123752000-123755600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:123752200-123753600	Weak transcription	Osteobl	bone
31	chr12:123752200-123753800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:123752200-123753800	Enhancers	NHDF-Ad	bronchial
33	chr12:123752200-123753800	Weak transcription	NHEK	skin
34	chr12:123752200-123754000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr12:123752200-123754000	Enhancers	Right Ventricle	heart
36	chr12:123752200-123755200	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr12:123752200-123755600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:123752200-123755600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr12:123752400-123753600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:123752400-123753800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr12:123752400-123754000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:123752400-123754000	Enhancers	Fetal Lung	lung
43	chr12:123752400-123754000	Enhancers	Placenta	Placenta
44	chr12:123752400-123754000	Enhancers	Left Ventricle	heart
45	chr12:123752400-123754200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr12:123752400-123754200	Flanking Active TSS	HSMM	muscle
47	chr12:123752400-123754400	Enhancers	Lung	lung
48	chr12:123752400-123755400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr12:123752400-123755600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr12:123752400-123755600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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