Variant report

Variant	rs258747
Chromosome Location	chr5:142656813-142656814
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	chr5:142655877..142658006-chr5:142659926..142661730,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10041520	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10482682	0.88[GIH][hapmap]
rs11750560	0.81[EUR][1000 genomes]
rs258763	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33383	0.87[ASW][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33388	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4634384	1.00[CEU][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6191	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6877893	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7716360	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs852976	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs852980	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs852983	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs853175	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853180	1.00[JPT][hapmap]
rs853183	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs864354	0.85[EUR][1000 genomes];0.85[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	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv5041	chr5:142653189-142697896	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs258747	PCDHB9	cis	cerebellum	SCAN
rs258747	SRA1	cis	cerebellum	SCAN
rs258747	PCDHB16	cis	cerebellum	SCAN
rs258747	LARS	cis	cerebellum	SCAN
rs258747	NR3C1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142642600-142658200	Weak transcription	Osteobl	bone
2	chr5:142643000-142658000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:142646600-142672400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:142647800-142658800	Weak transcription	Hela-S3	cervix
5	chr5:142649000-142658000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:142650000-142657200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:142650000-142674000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:142650200-142658000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr5:142650400-142658000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:142650600-142677200	Weak transcription	Aorta	Aorta
11	chr5:142650800-142659200	Weak transcription	Thymus	Thymus
12	chr5:142652200-142669800	Weak transcription	Left Ventricle	heart
13	chr5:142652400-142659400	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:142652800-142660200	Weak transcription	NH-A	brain
15	chr5:142653000-142658400	Weak transcription	Fetal Lung	lung
16	chr5:142653000-142671200	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:142653200-142658000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:142653200-142674800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:142654000-142659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:142654200-142659200	Weak transcription	HSMMtube	muscle
21	chr5:142654600-142659400	Strong transcription	GM12878-XiMat	blood
22	chr5:142654600-142666600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:142654800-142658200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:142654800-142658400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:142654800-142659400	Weak transcription	NHLF	lung
26	chr5:142654800-142663600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:142655000-142657000	Weak transcription	HMEC	breast
28	chr5:142655000-142664800	Weak transcription	NHEK	skin
29	chr5:142655000-142669800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:142655000-142671600	Weak transcription	K562	blood
31	chr5:142655200-142662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:142655200-142674000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:142655200-142674200	Weak transcription	Brain Angular Gyrus	brain
34	chr5:142655400-142661400	Weak transcription	Placenta	Placenta
35	chr5:142655400-142672600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:142655600-142658200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:142655600-142658800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:142655800-142657000	Weak transcription	Adipose Nuclei	Adipose
39	chr5:142655800-142658000	Weak transcription	Fetal Thymus	thymus
40	chr5:142655800-142658600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:142655800-142660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:142655800-142662000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:142655800-142664600	Strong transcription	NHDF-Ad	bronchial
44	chr5:142655800-142669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:142655800-142670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:142655800-142671800	Weak transcription	Psoas Muscle	Psoas
47	chr5:142655800-142677200	Weak transcription	Spleen	Spleen
48	chr5:142655800-142699200	Strong transcription	Dnd41	blood
49	chr5:142656000-142657200	Strong transcription	A549	lung
50	chr5:142656000-142658000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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