Variant report

Variant	rs12060228
Chromosome Location	chr1:210551543-210551544
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	TEAD4	chr1:210551110-210551778	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr1:210550088-210551772	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr1:210551293-210551638	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr1:210551057-210551710	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr1:210551085-210551786	SK-N-SH	brain:	n/a	n/a
6	EP300	chr1:210551059-210551806	SK-N-SH	brain:	n/a	chr1:210551672-210551682 chr1:210551062-210551076
7	NFIC	chr1:210551085-210551690	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr1:210550991-210551756	SK-N-SH	brain:	n/a	n/a
9	JUND	chr1:210550217-210551721	SK-N-SH	brain:	n/a	chr1:210550485-210550494
10	EP300	chr1:210551275-210551592	SK-N-SH_RA	brain:	n/a	n/a
11	JUND	chr1:210551153-210551815	SK-N-SH	brain:	n/a	n/a
12	RXRA	chr1:210551106-210551735	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr1:210551052-210551886	SK-N-SH	brain:	n/a	n/a
14	FOSL2	chr1:210551084-210551735	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:210551278-210551660	SK-N-SH	brain:	n/a	n/a
16	EP300	chr1:210550169-210551742	SK-N-SH	brain:	n/a	chr1:210551672-210551682 chr1:210551033-210551041 chr1:210551062-210551076 chr1:210550618-210550632
17	EP300	chr1:210551280-210551715	SK-N-SH_RA	brain:	n/a	chr1:210551672-210551682

No.	Distal block	Cell Line	Cell type
1	chr1:210549868..210552421-chr1:210574134..210576852,2	K562	blood:
2	chr1:210550399..210552265-chr1:210555579..210558136,2	MCF-7	breast:
3	chr1:210550122..210554367-chr1:210555411..210560476,4	K562	blood:
4	chr1:210540564..210542647-chr1:210551469..210554049,2	MCF-7	breast:
5	chr1:210502029..210504336-chr1:210551267..210553023,2	MCF-7	breast:
6	chr1:210551526..210553574-chr1:210572140..210575060,2	K562	blood:

Variant related genes	Relation type
RNU5A-8P	TF binding region
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11119477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11119478	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11119481	1.00[AMR][1000 genomes]
rs11119513	1.00[CHD][hapmap]
rs12087492	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17016283	1.00[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
2	chr1:210536800-210558800	Weak transcription	Fetal Stomach	stomach
3	chr1:210538400-210565600	Weak transcription	Esophagus	oesophagus
4	chr1:210543200-210555800	Weak transcription	Right Atrium	heart
5	chr1:210543200-210565200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:210546600-210566200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:210547600-210555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:210548600-210556000	Weak transcription	HepG2	liver
9	chr1:210548600-210566400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:210549600-210552600	Enhancers	HSMMtube	muscle
11	chr1:210549600-210552600	Enhancers	Osteobl	bone
12	chr1:210549600-210552800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:210549800-210552800	Enhancers	NHDF-Ad	bronchial
14	chr1:210550000-210552600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:210550000-210552800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:210550000-210553000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:210550200-210552600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:210550200-210553400	Enhancers	HSMM	muscle
19	chr1:210550200-210557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:210550400-210551600	Bivalent Enhancer	NHEK	skin
21	chr1:210551000-210551600	Flanking Active TSS	NH-A	brain
22	chr1:210551000-210551800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:210551000-210551800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:210551200-210552400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:210551200-210552400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:210551200-210552400	Weak transcription	NHLF	lung
27	chr1:210551200-210553000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:210551200-210566600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:210551400-210552400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:210551400-210552400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:210551400-210557600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:210551400-210586000	Weak transcription	Primary hematopoietic stem cells	blood

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