Variant report

Variant	rs1432641
Chromosome Location	chr5:127140455-127140456
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127140096..127141599-chr5:127143950..127145485,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1002214	0.81[AMR][1000 genomes]
rs10044507	0.98[ASN][1000 genomes]
rs10066288	0.81[AMR][1000 genomes]
rs10067219	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1067705	0.81[AMR][1000 genomes]
rs1092294	0.81[AMR][1000 genomes]
rs1213745	0.81[AMR][1000 genomes]
rs13155734	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356121	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1616107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2673770	0.81[AMR][1000 genomes]
rs6867166	1.00[ASW][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6878186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs711361	0.81[AMR][1000 genomes]
rs711363	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs711364	0.95[CEU][hapmap]
rs711369	0.81[AMR][1000 genomes]
rs7729013	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790829	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes]
rs790834	0.81[AMR][1000 genomes]
rs790839	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790840	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790841	0.80[AFR][1000 genomes]
rs796919	0.81[AMR][1000 genomes]
rs806464	0.81[AMR][1000 genomes]
rs810996	0.81[AMR][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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1432641	CTXN3	cis	parietal	SCAN
rs1432641	PRRC1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127135200-127143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:127138200-127140600	Weak transcription	HSMM	muscle
3	chr5:127138200-127140600	Weak transcription	HSMMtube	muscle
4	chr5:127138400-127141400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:127138400-127141800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:127138600-127140600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:127138600-127140600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:127138600-127140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:127138600-127146400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:127138800-127140600	Weak transcription	NHDF-Ad	bronchial
11	chr5:127138800-127140600	Weak transcription	NHLF	lung
12	chr5:127139000-127145600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:127139200-127151800	Weak transcription	Stomach Mucosa	stomach
14	chr5:127140000-127141800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:127140200-127142000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:127140400-127140800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:127140400-127140800	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:127140400-127140800	Enhancers	NHEK	skin

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