Variant report

Variant	rs12673676
Chromosome Location	chr7:108023164-108023165
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108022146..108024976-chr7:108095353..108098019,2	MCF-7	breast:
2	chr7:108018473..108020878-chr7:108021691..108023261,2	MCF-7	breast:
3	chr7:108019480..108021624-chr7:108021812..108023878,2	MCF-7	breast:
4	chr7:107997129..107999645-chr7:108022615..108024810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1016148	0.82[CEU][hapmap]
rs10487850	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10953563	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs10953568	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11763042	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11766336	0.89[ASW][hapmap];0.84[CEU][hapmap]
rs11769966	0.85[EUR][1000 genomes]
rs12538050	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12539964	0.81[MEX][hapmap]
rs12673082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap]
rs12705448	0.82[CEU][hapmap]
rs13221333	0.90[EUR][1000 genomes]
rs13242951	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs13243381	0.83[EUR][1000 genomes]
rs16872495	0.88[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs17155485	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs17155518	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17155522	0.87[EUR][1000 genomes]
rs1859765	0.89[ASW][hapmap];0.84[CEU][hapmap]
rs2158847	0.84[CEU][hapmap]
rs2267891	0.84[CEU][hapmap]
rs2300024	0.82[CEU][hapmap]
rs2300030	0.89[EUR][1000 genomes]
rs2395962	0.81[MEX][hapmap]
rs4142283	0.82[CEU][hapmap]
rs4727703	0.82[CEU][hapmap]
rs6956163	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7778203	0.90[EUR][1000 genomes]
rs969708	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12673676	RNF133	trans	parietal	SCAN
rs12673676	DNAJB9	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108014000-108023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:108016800-108023400	Weak transcription	Brain Angular Gyrus	brain
4	chr7:108017000-108023200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:108018400-108023400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:108018400-108023400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:108020000-108034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:108021400-108023400	Weak transcription	Brain Anterior Caudate	brain
9	chr7:108021400-108040800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:108021400-108043000	Weak transcription	HMEC	breast
11	chr7:108021800-108025000	Weak transcription	A549	lung
12	chr7:108021800-108026600	Weak transcription	HUVEC	blood vessel
13	chr7:108022400-108034200	Weak transcription	Pancreas	Pancrea
14	chr7:108022600-108023400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:108023000-108024000	Enhancers	Brain Inferior Temporal Lobe	brain

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