Variant report

Variant	rs959459
Chromosome Location	chr14:56771970-56771971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56769713..56772001-chr14:56773071..56775429,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10144612	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10483656	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12147737	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1427556	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17688725	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17688801	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs17689278	0.90[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17761563	1.00[CHD][hapmap]
rs17762499	0.90[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs17762733	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17769788	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17832675	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2035283	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2343376	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2343604	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28712711	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2880615	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs3850298	0.89[CEU][hapmap]
rs3912203	0.81[CEU][hapmap]
rs4127813	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs58502917	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8020301	0.91[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1044886	chr14:56689682-56834648	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv542104	chr14:56689682-56834648	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv901978	chr14:56740554-56799997	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv901979	chr14:56740554-56802610	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2638994	chr14:56771590-56773021	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs959459	PSMC6	cis	cerebellum	SCAN
rs959459	WDHD1	cis	cerebellum	SCAN
rs959459	C14orf166	cis	cerebellum	SCAN
rs959459	ERO1L	cis	parietal	SCAN
rs959459	ARID4A	cis	cerebellum	SCAN
rs959459	MAPK1IP1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56738800-56775600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:56750400-56777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:56753200-56773200	Weak transcription	Fetal Brain Male	brain
4	chr14:56757400-56773200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr14:56758800-56772400	Weak transcription	Brain Germinal Matrix	brain
6	chr14:56759000-56777000	Weak transcription	Left Ventricle	heart
7	chr14:56764400-56774400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr14:56764400-56785600	Weak transcription	Lung	lung
9	chr14:56764400-56798200	Weak transcription	Pancreas	Pancrea
10	chr14:56764400-56808800	Weak transcription	Thymus	Thymus
11	chr14:56765000-56772800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr14:56765200-56774800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr14:56765200-56776600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:56766400-56776800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:56767600-56777200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr14:56767800-56777200	Weak transcription	NH-A	brain
17	chr14:56768600-56784600	Weak transcription	Dnd41	blood
18	chr14:56769800-56776000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr14:56769800-56780200	Weak transcription	Primary B cells from cord blood	blood
20	chr14:56771600-56773600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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