Variant report

Variant	rs17209258
Chromosome Location	chr5:142673397-142673398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:142667219..142669950-chr5:142671988..142675283,3	K562	blood:
2	chr5:142667219..142669950-chr5:142672970..142675283,2	K562	blood:
3	chr5:142672258..142673872-chr5:142678279..142679872,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10482634	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10482655	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10482682	1.00[JPT][hapmap]
rs11745958	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750172	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17209216	0.85[AMR][1000 genomes]
rs17209237	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17209251	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17287745	0.93[ASN][1000 genomes]
rs17339455	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17399352	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2013935	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2398631	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2963156	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33944801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35501467	0.84[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs4912906	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4912908	0.84[EUR][1000 genomes]
rs4986593	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62375463	0.93[ASN][1000 genomes]
rs62375499	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62375502	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9324916	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17209258	RBM27	cis	parietal	SCAN
rs17209258	PCDHGC5	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142650000-142674000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:142650600-142677200	Weak transcription	Aorta	Aorta
3	chr5:142653200-142674800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:142655200-142674000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:142655200-142674200	Weak transcription	Brain Angular Gyrus	brain
6	chr5:142655800-142677200	Weak transcription	Spleen	Spleen
7	chr5:142655800-142699200	Strong transcription	Dnd41	blood
8	chr5:142656000-142677400	Weak transcription	Gastric	stomach
9	chr5:142656600-142677000	Weak transcription	Lung	lung
10	chr5:142657000-142674000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:142657800-142695400	Weak transcription	Pancreas	Pancrea
12	chr5:142658000-142679000	Weak transcription	Colonic Mucosa	Colon
13	chr5:142658200-142694800	Weak transcription	Right Ventricle	heart
14	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
15	chr5:142658800-142677400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:142659400-142677200	Weak transcription	HSMMtube	muscle
17	chr5:142659600-142674600	Weak transcription	HepG2	liver
18	chr5:142659600-142677400	Weak transcription	Ovary	ovary
19	chr5:142659800-142679400	Weak transcription	Small Intestine	intestine
20	chr5:142659800-142692600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:142661600-142677200	Weak transcription	HUVEC	blood vessel
22	chr5:142664000-142673800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:142664000-142674000	Weak transcription	Brain Substantia Nigra	brain
24	chr5:142664000-142677400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:142664000-142684600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:142664000-142685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:142664200-142674600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:142664400-142681200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:142664400-142693400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:142667200-142682000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:142667400-142688800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:142667800-142681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:142668000-142680200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:142668200-142680200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:142668600-142674800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr5:142668600-142678400	Strong transcription	A549	lung
37	chr5:142668600-142680400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:142668600-142680800	Strong transcription	NHDF-Ad	bronchial
39	chr5:142668600-142688800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:142668800-142676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:142668800-142678600	Weak transcription	Fetal Stomach	stomach
42	chr5:142668800-142682400	Strong transcription	GM12878-XiMat	blood
43	chr5:142668800-142693800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:142669000-142680800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:142669200-142680200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:142669400-142680400	Strong transcription	Osteobl	bone
47	chr5:142669600-142682600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr5:142669800-142674200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:142669800-142675200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:142669800-142675200	Strong transcription	Left Ventricle	heart

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