Variant report

Variant	rs2667385
Chromosome Location	chr15:83551313-83551314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83550002..83552945-chr15:83556510..83558401,2	MCF-7	breast:
2	chr15:83548836..83552018-chr15:83556203..83558359,3	K562	blood:
3	chr15:83521559..83523474-chr15:83548872..83551411,2	MCF-7	breast:
4	chr15:83548774..83553055-chr15:83557279..83560019,6	K562	blood:
5	chr15:83548573..83551400-chr15:83560401..83562858,2	MCF-7	breast:
6	chr15:83550326..83552965-chr15:83562801..83565043,2	K562	blood:
7	chr15:83549718..83551479-chr15:83574830..83576758,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10906985	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11259959	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[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	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553883	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs17360083	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2379992	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2621227	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]
rs2621228	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]
rs2667382	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667383	0.96[ASN][1000 genomes]
rs41310978	0.94[ASN][1000 genomes]
rs4238539	0.86[JPT][hapmap]
rs62011731	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011732	0.99[ASN][1000 genomes]
rs62011734	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168760	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169401	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9806543	0.85[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2667385	WHAMM	cis	Adipose Subcutaneous	GTEx
rs2667385	HOMER2	cis	Skin Sun Exposed Lower leg	GTEx
rs2667385	RASGRF1	cis	parietal	SCAN
rs2667385	RASGRF1	cis	cerebellum	SCAN
rs2667385	PSMA4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
3	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
4	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:83537000-83551400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
7	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
9	chr15:83542400-83564000	Weak transcription	Lung	lung
10	chr15:83542400-83567200	Weak transcription	Brain Angular Gyrus	brain
11	chr15:83542800-83558000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:83543000-83557600	Weak transcription	Fetal Stomach	stomach
13	chr15:83543600-83557800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:83543600-83558000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:83543600-83567600	Weak transcription	Aorta	Aorta
16	chr15:83544000-83558000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:83544000-83558000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:83544000-83563800	Weak transcription	Brain Anterior Caudate	brain
19	chr15:83544200-83557800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:83544200-83560800	Weak transcription	Primary T cells from cord blood	blood
21	chr15:83544800-83559400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:83545000-83551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:83549000-83551600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr15:83549200-83551400	Strong transcription	Liver	Liver
25	chr15:83549200-83551600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr15:83550200-83559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:83550400-83551600	Enhancers	HSMMtube	muscle
28	chr15:83550600-83551600	Genic enhancers	Pancreas	Pancrea
29	chr15:83550800-83551600	Enhancers	Gastric	stomach
30	chr15:83550800-83551600	Enhancers	Psoas Muscle	Psoas
31	chr15:83550800-83551600	Enhancers	HSMM	muscle
32	chr15:83551000-83551600	Enhancers	Fetal Muscle Trunk	muscle
33	chr15:83551000-83551600	Enhancers	Right Ventricle	heart
34	chr15:83551000-83551800	Enhancers	Fetal Muscle Leg	muscle

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