Variant report

Variant	rs2061947
Chromosome Location	chr15:83606232-83606233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83602779..83607624-chr15:83619045..83622811,4	MCF-7	breast:
2	chr15:83604502..83607500-chr15:83609162..83613049,3	K562	blood:
3	chr15:83564997..83567532-chr15:83604319..83607147,2	MCF-7	breast:
4	chr15:83601981..83604800-chr15:83605972..83608317,2	MCF-7	breast:
5	chr15:83586563..83590594-chr15:83604214..83607566,4	MCF-7	breast:
6	chr15:83603085..83606427-chr15:83619631..83622766,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1037403	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11259960	0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11259963	0.84[AMR][1000 genomes]
rs12050725	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12148275	0.80[ASW][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12441675	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1568657	0.89[JPT][hapmap]
rs2046070	0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap]
rs2123157	0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs2167602	0.94[JPT][hapmap]
rs4842917	0.94[ASN][1000 genomes]
rs4842935	0.94[JPT][hapmap]
rs4843141	1.00[JPT][hapmap]
rs4843144	0.80[JPT][hapmap];0.85[MKK][hapmap]
rs4843146	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs6603038	0.83[AMR][1000 genomes]
rs6603041	0.94[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap]
rs8034220	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8043020	0.94[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs872598	0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs872599	0.81[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2061947	WHAMM	cis	parietal	SCAN
rs2061947	C15orf40	cis	normal skin	skin_eQTL
rs2061947	BTBD1	cis	parietal	SCAN
rs2061947	CIB2	cis	cerebellum	SCAN

Chromatin state (count:28 , 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	chr15:83592600-83610600	Weak transcription	Liver	Liver
4	chr15:83598600-83608600	Enhancers	Pancreas	Pancrea
5	chr15:83602000-83608200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr15:83602600-83607600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr15:83602800-83607000	Enhancers	Gastric	stomach
8	chr15:83604600-83606600	Enhancers	Esophagus	oesophagus
9	chr15:83604800-83607200	Enhancers	Psoas Muscle	Psoas
10	chr15:83605000-83606400	Weak transcription	Spleen	Spleen
11	chr15:83605000-83606600	Enhancers	HSMM	muscle
12	chr15:83605200-83606600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:83605400-83606600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:83605400-83606600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:83605400-83606800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:83605600-83606600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:83605800-83606400	Enhancers	HMEC	breast
18	chr15:83605800-83606400	Enhancers	NHEK	skin
19	chr15:83605800-83606400	Enhancers	Osteobl	bone
20	chr15:83605800-83606600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:83605800-83606600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:83605800-83606600	Enhancers	Fetal Kidney	kidney
23	chr15:83605800-83606600	Enhancers	NH-A	brain
24	chr15:83606000-83606400	Flanking Active TSS	HSMMtube	muscle
25	chr15:83606000-83606600	Enhancers	Right Ventricle	heart
26	chr15:83606000-83606800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:83606200-83606600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:83606200-83611600	Weak transcription	A549	lung

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