Variant report

Variant	rs1549629
Chromosome Location	chr5:115669950-115669951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1031363	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1035370	0.83[AFR][1000 genomes]
rs17139218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs17139272	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs17139308	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17139323	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17139432	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17139507	1.00[EUR][1000 genomes]
rs17139559	0.84[AFR][1000 genomes]
rs2900096	1.00[CEU][hapmap]
rs4342363	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4392665	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4403214	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs58594358	1.00[AMR][1000 genomes]
rs60462627	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60647033	0.88[AFR][1000 genomes]
rs6861593	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6863773	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs6872204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6897052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7700792	0.84[AFR][1000 genomes]
rs7701626	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7701783	1.00[AMR][1000 genomes]
rs7706895	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7708270	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7714974	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7728830	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7729217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription 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	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1549629	FLJ23152	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115644400-115671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:115649000-115692800	Weak transcription	Fetal Heart	heart
3	chr5:115653600-115670400	Weak transcription	Right Ventricle	heart
4	chr5:115663200-115671000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:115664600-115671600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:115665200-115671800	Weak transcription	Ovary	ovary
7	chr5:115665600-115670400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:115665800-115671000	Weak transcription	Primary T cells from cord blood	blood
9	chr5:115666400-115670000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:115666800-115683600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:115668400-115671400	Weak transcription	Stomach Mucosa	stomach
12	chr5:115668800-115670600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr5:115668800-115670800	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr5:115668800-115671000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:115669200-115670400	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr5:115669400-115670400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr5:115669400-115670800	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:115669600-115670000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:115669600-115670000	Strong transcription	Dnd41	blood
20	chr5:115669600-115670200	ZNF genes & repeats	Liver	Liver
21	chr5:115669600-115670200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr5:115669600-115670200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr5:115669600-115670200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr5:115669600-115670400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
25	chr5:115669600-115670400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:115669600-115670400	ZNF genes & repeats	Aorta	Aorta
27	chr5:115669600-115670400	Strong transcription	Fetal Kidney	kidney
28	chr5:115669600-115670400	ZNF genes & repeats	Left Ventricle	heart
29	chr5:115669600-115670600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr5:115669600-115670600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:115669600-115670600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:115669600-115670600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:115669600-115670600	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr5:115669600-115670600	ZNF genes & repeats	Placenta	Placenta
35	chr5:115669600-115670600	ZNF genes & repeats	Gastric	stomach
36	chr5:115669600-115670600	ZNF genes & repeats	Thymus	Thymus
37	chr5:115669600-115670600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr5:115669600-115670800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:115669600-115670800	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr5:115669600-115670800	ZNF genes & repeats	Esophagus	oesophagus
41	chr5:115669800-115670000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:115669800-115670000	ZNF genes & repeats	Fetal Lung	lung
43	chr5:115669800-115670200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
44	chr5:115669800-115670400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr5:115669800-115670600	ZNF genes & repeats	Fetal Stomach	stomach
46	chr5:115669800-115670800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:115669800-115670800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:115669800-115670800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:115669800-115670800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:115669800-115670800	ZNF genes & repeats	Pancreas	Pancrea

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