Variant report

Variant	rs17608902
Chromosome Location	chr5:127716567-127716568
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10519991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10520002	1.00[YRI][hapmap]
rs1366455	1.00[YRI][hapmap]
rs154001	0.86[CHB][hapmap]
rs154003	1.00[CHB][hapmap]
rs17676837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676891	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255725	1.00[CHB][hapmap]
rs255730	1.00[CHB][hapmap]
rs27913	0.85[CHB][hapmap]
rs34806635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364671	1.00[CHB][hapmap]
rs468026	1.00[CHB][hapmap]
rs468182	1.00[CHB][hapmap]
rs468200	1.00[CHB][hapmap]
rs468229	1.00[CHB][hapmap]
rs56090677	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Migraine - clinic-based	23793025	GWAS catalog
Migraine with aura	23793025	GWAS catalog

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
2	chr5:127675600-127742200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:127679200-127731200	Weak transcription	Right Ventricle	heart
4	chr5:127685400-127725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:127686000-127738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:127686000-127742000	Weak transcription	A549	lung
7	chr5:127690200-127724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:127695200-127737800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:127696800-127738200	Weak transcription	Fetal Lung	lung
10	chr5:127700600-127719600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:127704800-127741800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:127705000-127724800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:127705000-127730200	Weak transcription	Fetal Intestine Large	intestine
14	chr5:127705200-127718000	Weak transcription	Ovary	ovary
15	chr5:127705200-127724800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:127705600-127722000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:127705800-127731200	Weak transcription	Left Ventricle	heart
18	chr5:127710600-127724200	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:127711200-127724800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:127711200-127724800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:127712800-127723800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:127712800-127725000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:127713200-127718000	Weak transcription	Fetal Heart	heart
24	chr5:127713200-127724800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:127713200-127725000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:127713200-127727600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:127713600-127724800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:127714200-127724000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:127714600-127743000	Weak transcription	HMEC	breast
30	chr5:127714800-127718800	Weak transcription	NHEK	skin
31	chr5:127715000-127719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:127715400-127719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:127715800-127716600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:127715800-127720400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:127715800-127724800	Weak transcription	Fetal Stomach	stomach
36	chr5:127716000-127720800	Weak transcription	Placenta	Placenta
37	chr5:127716000-127724400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:127716000-127724600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:127716200-127716600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:127716200-127716600	Enhancers	Fetal Kidney	kidney
41	chr5:127716400-127725000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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