Variant report

Variant	rs2621227
Chromosome Location	chr15:83558512-83558513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83558429..83560638-chr15:83611658..83613627,2	MCF-7	breast:
2	chr15:83537400..83539561-chr15:83557067..83559274,2	MCF-7	breast:
3	chr15:83558288..83561120-chr15:83563049..83565497,2	MCF-7	breast:
4	chr15:83548774..83553055-chr15:83557279..83560019,6	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10906985	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11259959	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12385964	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1256429	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1256434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1256452	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1256453	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256455	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12905235	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs13380133	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553883	0.86[JPT][hapmap]
rs17360083	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2379992	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2621228	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667382	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667383	0.96[ASN][1000 genomes]
rs2667385	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310978	0.94[ASN][1000 genomes]
rs4238539	0.88[JPT][hapmap]
rs62011731	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011732	0.99[ASN][1000 genomes]
rs62011734	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168760	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169401	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9806543	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2621227	WHAMM	cis	Adipose Subcutaneous	GTEx
rs2621227	HOMER2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
3	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
5	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
7	chr15:83542400-83564000	Weak transcription	Lung	lung
8	chr15:83542400-83567200	Weak transcription	Brain Angular Gyrus	brain
9	chr15:83543600-83567600	Weak transcription	Aorta	Aorta
10	chr15:83544000-83563800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:83544200-83560800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:83544800-83559400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:83550200-83559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:83554400-83564000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:83556000-83563800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:83556800-83563800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:83557400-83563800	Weak transcription	Brain Substantia Nigra	brain
18	chr15:83557600-83558800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
19	chr15:83557600-83559200	Strong transcription	Fetal Stomach	stomach
20	chr15:83557600-83559400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
21	chr15:83557600-83560000	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:83557600-83560200	Enhancers	Fetal Muscle Leg	muscle
23	chr15:83557600-83560600	Genic enhancers	Pancreas	Pancrea
24	chr15:83557800-83558600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:83557800-83558600	Enhancers	Psoas Muscle	Psoas
26	chr15:83557800-83558800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:83557800-83561400	Strong transcription	Liver	Liver
28	chr15:83558000-83558600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:83558000-83558600	ZNF genes & repeats	Esophagus	oesophagus
30	chr15:83558000-83559200	Strong transcription	Gastric	stomach
31	chr15:83558000-83559400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:83558000-83559600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:83558000-83563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:83558200-83558600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:83558200-83560400	Enhancers	HSMMtube	muscle
36	chr15:83558200-83563800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:83558200-83563800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:83558200-83563800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:83558200-83564000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:83558200-83565000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:83558400-83563600	Weak transcription	HSMM	muscle
42	chr15:83558400-83569600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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