Variant report

Variant	rs12442894
Chromosome Location	chr15:83602849-83602850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83595241..83598969-chr15:83601777..83604663,4	MCF-7	breast:
2	chr15:83602779..83607624-chr15:83619045..83622811,4	MCF-7	breast:
3	chr15:83596164..83597844-chr15:83602191..83603903,2	MCF-7	breast:
4	chr15:83601981..83604800-chr15:83605972..83608317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1010820	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045742	0.82[CEU][hapmap]
rs1075619	0.82[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs1105714	1.00[ASN][1000 genomes]
rs11259957	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856299	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858162	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11858468	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12437558	0.82[EUR][1000 genomes]
rs12437858	0.81[EUR][1000 genomes]
rs12437901	0.82[EUR][1000 genomes]
rs12438575	0.82[EUR][1000 genomes]
rs12440265	0.94[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs12441006	0.82[EUR][1000 genomes]
rs12441575	0.82[EUR][1000 genomes]
rs17358518	1.00[ASN][1000 genomes]
rs17359001	0.86[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359494	0.82[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs17361375	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17567151	0.82[CEU][hapmap]
rs2019208	1.00[ASN][1000 genomes]
rs2034618	0.82[CEU][hapmap]
rs2055891	1.00[ASN][1000 genomes]
rs55800901	1.00[ASN][1000 genomes]
rs58396076	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60819629	0.82[EUR][1000 genomes]
rs62010162	0.82[EUR][1000 genomes]
rs62010164	0.82[EUR][1000 genomes]
rs62010165	0.82[EUR][1000 genomes]
rs62010166	0.82[EUR][1000 genomes]
rs62010173	0.82[EUR][1000 genomes]
rs62010174	0.81[EUR][1000 genomes]
rs62010175	0.82[EUR][1000 genomes]
rs62010177	0.81[EUR][1000 genomes]
rs62011706	1.00[ASN][1000 genomes]
rs62011709	1.00[ASN][1000 genomes]
rs62011712	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011735	1.00[ASN][1000 genomes]
rs62011742	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011744	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66619192	0.82[EUR][1000 genomes]
rs66757932	0.81[EUR][1000 genomes]
rs67022650	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179000	1.00[ASN][1000 genomes]
rs72753993	1.00[ASN][1000 genomes]
rs8031723	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv12334	chr15:83602318-83604788	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12442894	WHAMM	cis	parietal	SCAN
rs12442894	C15orf40	cis	parietal	SCAN
rs12442894	BTBD1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83586600-83619400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:83588800-83611600	Weak transcription	Right Atrium	heart
3	chr15:83589600-83605400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:83592600-83610600	Weak transcription	Liver	Liver
5	chr15:83593600-83604800	Weak transcription	Psoas Muscle	Psoas
6	chr15:83598600-83608600	Enhancers	Pancreas	Pancrea
7	chr15:83599600-83606200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:83600200-83603000	Weak transcription	HSMMtube	muscle
9	chr15:83600200-83606000	Weak transcription	Right Ventricle	heart
10	chr15:83600800-83603400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:83602000-83608200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr15:83602400-83603000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:83602400-83603000	Enhancers	Spleen	Spleen
14	chr15:83602600-83603400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr15:83602600-83603400	Enhancers	HSMM	muscle
16	chr15:83602600-83604200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:83602600-83605400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:83602600-83607600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:83602800-83603200	Enhancers	Fetal Muscle Trunk	muscle
20	chr15:83602800-83603600	Enhancers	Brain Angular Gyrus	brain
21	chr15:83602800-83604200	Enhancers	Esophagus	oesophagus
22	chr15:83602800-83605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:83602800-83607000	Enhancers	Gastric	stomach

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