Variant report

Variant	rs1343629
Chromosome Location	chr1:114106209-114106210
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10858002	0.81[LWK][hapmap]
rs11102658	0.85[AFR][1000 genomes]
rs1113523	0.81[YRI][hapmap]
rs12021513	0.84[AFR][1000 genomes]
rs12039224	0.85[AFR][1000 genomes]
rs1217204	0.82[YRI][hapmap]
rs1217216	0.91[ASN][1000 genomes]
rs1217222	0.90[ASN][1000 genomes]
rs1217225	0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs1217226	0.82[YRI][hapmap]
rs1217227	0.82[YRI][hapmap]
rs1217228	0.82[YRI][hapmap]
rs1217231	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1418957	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2153977	0.81[LWK][hapmap]
rs35390985	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4259646	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537790	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs6689879	0.88[YRI][hapmap]
rs6704188	0.85[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7511816	0.82[ASN][1000 genomes]
rs7522138	0.84[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7554019	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv947128	chr1:114088844-114122533	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1343629	PHTF1	cis	cerebellum	SCAN
rs1343629	BCL2L15	cis	cerebellum	SCAN
rs1343629	MAGI3	cis	cerebellum	SCAN
rs1343629	DCLRE1B	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114083400-114110000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:114088600-114109800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:114094800-114138400	Weak transcription	NHDF-Ad	bronchial
4	chr1:114095600-114108200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:114096400-114108800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:114098600-114106600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:114100200-114127600	Weak transcription	Ovary	ovary
8	chr1:114100600-114106600	Weak transcription	Aorta	Aorta
9	chr1:114100600-114107600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:114100600-114108200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:114100600-114108800	Weak transcription	Fetal Lung	lung
12	chr1:114100600-114112600	Weak transcription	Esophagus	oesophagus
13	chr1:114100600-114118200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:114100600-114118600	Weak transcription	Lung	lung
15	chr1:114100600-114118800	Weak transcription	Pancreas	Pancrea
16	chr1:114100600-114140200	Weak transcription	Left Ventricle	heart
17	chr1:114100600-114173400	Weak transcription	Gastric	stomach
18	chr1:114100800-114109600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:114101000-114112600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:114102800-114107800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:114105600-114109600	Weak transcription	Right Ventricle	heart

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