Variant report

Variant	rs2621228
Chromosome Location	chr15:83559954-83559955
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	chr15:83558288..83561120-chr15:83563049..83565497,2	MCF-7	breast:
3	chr15:83548774..83553055-chr15:83557279..83560019,6	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10906985	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11259959	0.83[AMR][1000 genomes];0.88[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];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1256434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[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	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256455	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12905235	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs13380133	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553883	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs17360083	0.92[ASW][hapmap];0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2379992	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2621227	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];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667383	0.96[ASN][1000 genomes]
rs2667385	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310978	0.94[ASN][1000 genomes]
rs4238539	0.86[JPT][hapmap]
rs62011731	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011732	0.99[ASN][1000 genomes]
rs62011734	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168760	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169401	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9806543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2621228	WHAMM	cis	Adipose Subcutaneous	GTEx
rs2621228	C15orf26	cis	cerebellum	SCAN
rs2621228	HOMER2	cis	Skin Sun Exposed Lower leg	GTEx
rs2621228	PSMA4	cis	cerebellum	SCAN
rs2621228	BTBD1	cis	cerebellum	SCAN
rs2621228	RASGRF1	cis	cerebellum	SCAN

Chromatin state (count:44 , 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	chr15:83554400-83564000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:83556000-83563800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:83556800-83563800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:83557400-83563800	Weak transcription	Brain Substantia Nigra	brain
16	chr15:83557600-83560000	Enhancers	Fetal Muscle Trunk	muscle
17	chr15:83557600-83560200	Enhancers	Fetal Muscle Leg	muscle
18	chr15:83557600-83560600	Genic enhancers	Pancreas	Pancrea
19	chr15:83557800-83561400	Strong transcription	Liver	Liver
20	chr15:83558000-83563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:83558200-83560400	Enhancers	HSMMtube	muscle
22	chr15:83558200-83563800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:83558200-83563800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:83558200-83563800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:83558200-83564000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:83558200-83565000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:83558400-83563600	Weak transcription	HSMM	muscle
28	chr15:83558400-83569600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:83558600-83561600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:83558600-83563600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:83558600-83566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:83558600-83567800	Weak transcription	Psoas Muscle	Psoas
33	chr15:83558800-83560600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr15:83558800-83562000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:83559000-83560000	Enhancers	Colon Smooth Muscle	Colon
36	chr15:83559200-83560000	Weak transcription	Gastric	stomach
37	chr15:83559200-83560000	Enhancers	Rectal Smooth Muscle	rectum
38	chr15:83559200-83560400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:83559200-83560400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:83559200-83563800	Weak transcription	Fetal Stomach	stomach
41	chr15:83559400-83560400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr15:83559400-83561000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:83559600-83563800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:83559600-83570200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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