Variant report

Variant	rs1010820
Chromosome Location	chr15:83614954-83614955
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83614588..83616160-chr15:83629650..83631536,2	K562	blood:
2	chr15:83614554..83618167-chr15:83619442..83621766,3	K562	blood:
3	chr15:83613181..83617398-chr15:83653354..83656044,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103942	Chromatin interaction
ENSG00000169612	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1045742	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs1075619	0.82[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs1105714	1.00[ASN][1000 genomes]
rs11259957	1.00[ASN][1000 genomes]
rs11856299	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs11858162	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11858377	0.82[CEU][hapmap];0.96[TSI][hapmap]
rs11858468	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12437558	0.84[EUR][1000 genomes]
rs12437858	0.83[EUR][1000 genomes]
rs12437901	0.84[EUR][1000 genomes]
rs12438575	0.84[EUR][1000 genomes]
rs12440265	0.94[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs12440386	0.93[TSI][hapmap]
rs12441006	0.84[EUR][1000 genomes]
rs12441575	0.84[EUR][1000 genomes]
rs12442894	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]
rs17358518	1.00[ASN][1000 genomes]
rs17359001	0.82[CEU][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs17359494	0.82[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs17361375	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[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]
rs41326445	0.82[CEU][hapmap];0.96[TSI][hapmap]
rs55800901	1.00[ASN][1000 genomes]
rs58396076	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60819629	0.84[EUR][1000 genomes]
rs62010162	0.84[EUR][1000 genomes]
rs62010164	0.84[EUR][1000 genomes]
rs62010165	0.84[EUR][1000 genomes]
rs62010166	0.84[EUR][1000 genomes]
rs62010170	0.82[EUR][1000 genomes]
rs62010172	0.80[EUR][1000 genomes]
rs62010173	0.84[EUR][1000 genomes]
rs62010174	0.83[EUR][1000 genomes]
rs62010175	0.84[EUR][1000 genomes]
rs62010177	0.83[EUR][1000 genomes]
rs62011706	1.00[ASN][1000 genomes]
rs62011709	1.00[ASN][1000 genomes]
rs62011712	1.00[ASN][1000 genomes]
rs62011735	1.00[ASN][1000 genomes]
rs62011742	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011744	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66619192	0.84[EUR][1000 genomes]
rs66757932	0.83[EUR][1000 genomes]
rs67022650	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716886	0.85[GIH][hapmap]
rs7177462	0.85[GIH][hapmap]
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];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs8043224	0.82[CEU][hapmap];0.96[TSI][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1010820	C15orf40	cis	parietal	SCAN
rs1010820	BTBD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83586600-83619400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:83606600-83618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:83606600-83620000	Weak transcription	Right Ventricle	heart
4	chr15:83611400-83619800	Weak transcription	Esophagus	oesophagus
5	chr15:83611800-83620400	Weak transcription	Right Atrium	heart
6	chr15:83612200-83617800	Weak transcription	Lung	lung
7	chr15:83612200-83618200	Weak transcription	Liver	Liver
8	chr15:83612200-83619200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:83612200-83619800	Weak transcription	HSMMtube	muscle
10	chr15:83612600-83617800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:83612600-83619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:83613400-83615000	Weak transcription	Psoas Muscle	Psoas
13	chr15:83613400-83619800	Weak transcription	Brain Anterior Caudate	brain
14	chr15:83613800-83615000	Weak transcription	Gastric	stomach
15	chr15:83613800-83615000	Weak transcription	Pancreas	Pancrea
16	chr15:83613800-83619800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:83614000-83619000	Weak transcription	Fetal Kidney	kidney
18	chr15:83614400-83615800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:83614600-83616800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:83614800-83618200	Enhancers	Skeletal Muscle Male	skeletal muscle

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