Variant report

Variant	rs829120
Chromosome Location	chr12:51236501-51236502
allele	C/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	TAF1	chr12:51236458-51237005	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:51236408-51236994	H1-hESC	embryonic stem cell:	n/a	n/a
3	YY1	chr12:51236361-51237037	H1-hESC	embryonic stem cell:	n/a	chr12:51236719-51236731 chr12:51236720-51236742 chr12:51236721-51236729 chr12:51236720-51236730 chr12:51236723-51236731
4	YY1	chr12:51236448-51236981	H1-hESC	embryonic stem cell:	n/a	chr12:51236719-51236731 chr12:51236720-51236742 chr12:51236721-51236729 chr12:51236720-51236730 chr12:51236723-51236731
5	RAD21	chr12:51236478-51237057	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr12:51236352-51237027	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr12:51236351-51237087	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr12:51236500-51236650	HCM	heart:	n/a	n/a
9	E2F6	chr12:51236271-51237132	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr12:51236369-51236899	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RN7SL519P	TF binding region
TMPRSS12	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10160844	0.81[ASN][1000 genomes]
rs10459237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10459238	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs10459239	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs10747595	0.85[ASN][1000 genomes]
rs10747596	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747597	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747599	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10783393	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783395	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs10783404	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10783405	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs10783406	1.00[CHB][hapmap]
rs10876099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876105	0.82[ASN][1000 genomes]
rs10876115	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876119	0.83[ASN][1000 genomes]
rs1096030	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1096031	0.83[ASN][1000 genomes]
rs1103441	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11169587	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs11169588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169592	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169602	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169603	0.80[ASN][1000 genomes]
rs11169608	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169609	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169610	0.85[ASN][1000 genomes]
rs11169612	0.85[ASN][1000 genomes]
rs11169614	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11495280	0.87[CEU][hapmap];0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs11533636	0.84[ASN][1000 genomes]
rs12578465	0.84[ASN][1000 genomes]
rs12578466	0.84[ASN][1000 genomes]
rs12581103	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1362964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1583697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1631348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1642997	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1643004	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1659375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2554852	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554854	0.84[ASN][1000 genomes]
rs3752667	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4483656	0.84[ASN][1000 genomes]
rs4768926	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768937	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4768938	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4768939	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73100855	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979616	0.85[ASN][1000 genomes]
rs829122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829128	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs829129	0.82[ASN][1000 genomes]
rs829131	1.00[CHB][hapmap]
rs829132	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs829139	0.82[ASN][1000 genomes]
rs829141	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs829142	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs829143	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs829144	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs844175	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs860476	0.82[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51228400-51236600	Weak transcription	Gastric	stomach
2	chr12:51233400-51236600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:51235000-51236800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:51235200-51236600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:51235200-51236600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:51236000-51236600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:51236200-51237200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:51236200-51237400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:51236200-51237400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr12:51236400-51236600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:51236400-51236600	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:51236400-51236600	Enhancers	Aorta	Aorta
13	chr12:51236400-51236600	Active TSS	Esophagus	oesophagus
14	chr12:51236400-51236600	Flanking Active TSS	Fetal Intestine Small	intestine
15	chr12:51236400-51236600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr12:51236400-51236600	Enhancers	Lung	lung
17	chr12:51236400-51236600	Enhancers	Right Atrium	heart
18	chr12:51236400-51236800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:51236400-51236800	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr12:51236400-51236800	Enhancers	Psoas Muscle	Psoas
21	chr12:51236400-51236800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:51236400-51237000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:51236400-51237000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:51236400-51237000	Active TSS	Fetal Heart	heart
25	chr12:51236400-51237000	Flanking Active TSS	Pancreas	Pancrea
26	chr12:51236400-51237000	Flanking Active TSS	NHEK	skin
27	chr12:51236400-51237200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:51236400-51237200	Active TSS	Fetal Kidney	kidney
29	chr12:51236400-51237200	Active TSS	Fetal Lung	lung
30	chr12:51236400-51237400	Active TSS	Placenta	Placenta
31	chr12:51236400-51237600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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