Variant report

Variant	rs13189231
Chromosome Location	chr5:178333337-178333338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10036425	0.90[ASN][1000 genomes]
rs10043786	0.90[ASN][1000 genomes]
rs10070619	1.00[JPT][hapmap]
rs1046724	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11249600	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11744810	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11745435	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11748636	0.95[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11749871	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11955491	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11955549	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11956161	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11959507	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12516516	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13166562	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13171869	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13172044	1.00[JPT][hapmap]
rs13182467	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183468	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13189941	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1566105	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17652441	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1826863	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1845939	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2047356	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34904538	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35123052	0.85[ASN][1000 genomes]
rs35245718	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35869073	0.90[ASN][1000 genomes]
rs35974815	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35984063	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55841430	0.90[ASN][1000 genomes]
rs6600996	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6894647	0.84[AMR][1000 genomes]
rs6897952	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs7445002	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7448421	1.00[ASW][hapmap];0.95[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7448445	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7722159	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7722441	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7735200	1.00[JPT][hapmap]
rs953741	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13189231	TMED9	cis	parietal	SCAN
rs13189231	BTNL9	cis	cerebellum	SCAN
rs13189231	EIF4E1B	cis	cerebellum	SCAN
rs13189231	TRIM52	cis	parietal	SCAN
rs13189231	B4GALT7	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178323600-178335400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:178323800-178333800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr5:178323800-178336200	Weak transcription	Right Ventricle	heart
4	chr5:178323800-178336400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:178328000-178334400	Weak transcription	Psoas Muscle	Psoas
6	chr5:178332400-178333400	ZNF genes & repeats	Fetal Brain Female	brain
7	chr5:178332400-178333400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr5:178332400-178334600	ZNF genes & repeats	Liver	Liver
9	chr5:178332600-178333400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:178332600-178333400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:178332800-178333400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr5:178332800-178333400	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr5:178332800-178333400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr5:178332800-178333400	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr5:178332800-178333400	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr5:178332800-178333400	Strong transcription	Brain Cingulate Gyrus	brain
17	chr5:178332800-178333400	ZNF genes & repeats	Brain Hippocampus Middle	brain
18	chr5:178332800-178333400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
19	chr5:178332800-178333400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:178332800-178333400	ZNF genes & repeats	Brain Substantia Nigra	brain
21	chr5:178332800-178333400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr5:178332800-178333400	ZNF genes & repeats	Fetal Lung	lung
23	chr5:178332800-178333400	ZNF genes & repeats	Placenta	Placenta
24	chr5:178332800-178333400	ZNF genes & repeats	Gastric	stomach
25	chr5:178332800-178333400	Strong transcription	Left Ventricle	heart
26	chr5:178332800-178333400	ZNF genes & repeats	Pancreas	Pancrea
27	chr5:178332800-178334200	ZNF genes & repeats	Fetal Stomach	stomach
28	chr5:178332800-178334200	ZNF genes & repeats	Ovary	ovary
29	chr5:178332800-178334400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr5:178333000-178333600	ZNF genes & repeats	Dnd41	blood
31	chr5:178333000-178334200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:178333000-178334200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:178333000-178335800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:178333200-178333400	Strong transcription	Brain Angular Gyrus	brain
35	chr5:178333200-178333400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr5:178333200-178333800	Weak transcription	Colonic Mucosa	Colon

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