Variant report

Variant	rs4546432
Chromosome Location	chr5:40682550-40682551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10060234	0.87[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs171605	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs249414	0.87[CEU][hapmap]
rs249422	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs249425	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs29742	0.86[CEU][hapmap];0.89[YRI][hapmap]
rs29743	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs29744	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs4133101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs4314453	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434778	0.87[CEU][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap]
rs4383756	0.87[CEU][hapmap]
rs4412150	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4434423	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs447810	0.87[CEU][hapmap]
rs4607392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451535	0.87[CEU][hapmap]
rs6871999	0.83[AFR][1000 genomes]
rs7726237	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4546432	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs4546432	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40678400-40683800	Active TSS	HSMM	muscle
2	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
3	chr5:40678600-40684400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:40678600-40685800	Active TSS	Right Atrium	heart
5	chr5:40678800-40683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:40679000-40685600	Active TSS	Colon Smooth Muscle	Colon
7	chr5:40679000-40689400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:40679200-40684000	Active TSS	Small Intestine	intestine
9	chr5:40679200-40684600	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr5:40679200-40684800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:40679200-40685000	Active TSS	NHLF	lung
12	chr5:40679400-40683600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr5:40679400-40684400	Active TSS	Primary T cells fromperipheralblood	blood
14	chr5:40679400-40684400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:40680000-40682600	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr5:40680000-40685000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:40680200-40683800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr5:40680200-40689600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr5:40680400-40682600	Flanking Active TSS	NH-A	brain
20	chr5:40680400-40684000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr5:40680800-40685200	Weak transcription	A549	lung
22	chr5:40680800-40690800	Transcr. at gene 5' and 3'	Dnd41	blood
23	chr5:40681000-40682600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:40681000-40682600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr5:40681000-40682600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr5:40681000-40682800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
27	chr5:40681200-40682600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:40681200-40682600	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:40681200-40682600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:40681200-40683000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:40681200-40683800	Active TSS	Stomach Mucosa	stomach
32	chr5:40681400-40683000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
33	chr5:40681400-40684600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
34	chr5:40681600-40682600	Active TSS	Osteobl	bone
35	chr5:40681600-40682800	Active TSS	Brain Cingulate Gyrus	brain
36	chr5:40681600-40682800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
37	chr5:40681600-40682800	Bivalent/Poised TSS	Psoas Muscle	Psoas
38	chr5:40681600-40683000	Bivalent/Poised TSS	Fetal Lung	lung
39	chr5:40681600-40684600	Active TSS	Fetal Kidney	kidney
40	chr5:40681600-40685200	Active TSS	Fetal Thymus	thymus
41	chr5:40681800-40682600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
42	chr5:40681800-40682600	Active TSS	Brain Hippocampus Middle	brain
43	chr5:40681800-40682800	Bivalent/Poised TSS	Left Ventricle	heart
44	chr5:40681800-40683000	Flanking Active TSS	HMEC	breast
45	chr5:40681800-40684000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:40681800-40685800	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr5:40682000-40682600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
48	chr5:40682000-40682800	Active TSS	Lung	lung
49	chr5:40682000-40682800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr5:40682000-40683000	Flanking Active TSS	Primary B cells from peripheral blood	blood

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