Variant report

Variant	rs10876098
Chromosome Location	chr12:51220373-51220374
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51212786..51214358-chr12:51219133..51221117,2	K562	blood:
2	chr12:51218257..51221554-chr12:51475850..51478812,3	MCF-7	breast:
3	chr12:51216774..51221510-chr12:51379576..51384198,5	MCF-7	breast:
4	chr12:51218193..51220790-chr12:51416290..51419028,2	K562	blood:
5	chr12:51218097..51220673-chr12:51419291..51422139,4	MCF-7	breast:
6	chr12:51216775..51221102-chr12:51419333..51421670,3	K562	blood:
7	chr12:51219096..51220890-chr12:51222074..51224257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10783387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876084	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10876087	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876092	0.85[EUR][1000 genomes]
rs11169523	0.83[CHB][hapmap]
rs11169524	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs11169562	0.84[EUR][1000 genomes]
rs11169563	0.87[EUR][1000 genomes]
rs11169567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169570	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169572	0.88[EUR][1000 genomes]
rs11169578	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1129406	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11503907	0.81[EUR][1000 genomes]
rs12372718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12427378	0.83[CHB][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs12818741	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1316607	0.83[CHB][hapmap];0.93[TSI][hapmap]
rs13378012	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2090852	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2139930	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs2280503	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs34645899	0.90[EUR][1000 genomes]
rs34863430	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35353300	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742062	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs4307773	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4388959	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs4768903	0.82[TSI][hapmap]
rs4986838	0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61926303	0.87[EUR][1000 genomes]
rs7133974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7137845	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7304335	0.88[EUR][1000 genomes]
rs7306677	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs864899	0.92[CEU][hapmap]
rs876080	0.90[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs9943712	0.81[AMR][1000 genomes];0.83[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10876098	ATF1	cis	Artery Tibial	GTEx
rs10876098	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs10876098	ATF1	cis	Esophagus Muscularis	GTEx
rs10876098	ATF1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:51205000-51228200	Weak transcription	Gastric	stomach
3	chr12:51210200-51222000	Weak transcription	Esophagus	oesophagus
4	chr12:51210600-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:51210600-51223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:51211000-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:51211000-51222000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:51213200-51222200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:51213400-51221800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:51213400-51222600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:51213800-51222800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51217800-51220400	Weak transcription	Psoas Muscle	Psoas
13	chr12:51218800-51223400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:51219200-51221800	Weak transcription	HMEC	breast
15	chr12:51219200-51223000	Weak transcription	Brain Anterior Caudate	brain
16	chr12:51219400-51222400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:51219600-51222200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:51219600-51222400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:51219600-51222800	Weak transcription	Thymus	Thymus
20	chr12:51220200-51222200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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