Variant report

Variant	rs7349100
Chromosome Location	chr1:210830589-210830590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210829972..210830727-chr4:175163977..175164893,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11119556	0.94[ASN][1000 genomes]
rs11119561	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119562	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121954	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122067	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[MKK][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12123726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125545	0.81[CHD][hapmap]
rs12129019	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133319	0.82[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12401773	0.91[ASN][1000 genomes]
rs2078224	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs34771900	0.91[ASN][1000 genomes]
rs4282879	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs4328122	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626957	0.91[CHB][hapmap]
rs4638190	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72468063	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv522480	chr1:210779936-210848344	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
3	esv1825229	chr1:210789477-210854976	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
4	nsv873150	chr1:210808270-210893233	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv873151	chr1:210818347-210846888	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv873152	chr1:210820285-210854815	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7349100	CD34	cis	parietal	SCAN
rs7349100	C1orf107	cis	cerebellum	SCAN
rs7349100	LPGAT1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210821400-210837000	Weak transcription	Left Ventricle	heart
2	chr1:210827400-210837200	Weak transcription	Right Ventricle	heart
3	chr1:210827600-210830600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:210827600-210830600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:210827600-210830600	Weak transcription	Fetal Lung	lung
6	chr1:210827600-210831000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:210827600-210831200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:210827600-210831800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:210827600-210836400	Weak transcription	Fetal Heart	heart
10	chr1:210827600-210836800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:210827600-210837000	Weak transcription	Gastric	stomach
12	chr1:210827600-210843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:210827600-210847600	Weak transcription	HSMM	muscle
14	chr1:210829000-210853400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:210829400-210831600	Strong transcription	HSMMtube	muscle
16	chr1:210829800-210831800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:210830000-210831800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:210830200-210831600	Enhancers	Brain Hippocampus Middle	brain
19	chr1:210830400-210830800	Enhancers	Brain Anterior Caudate	brain
20	chr1:210830400-210831200	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:210830400-210831600	Enhancers	Brain Substantia Nigra	brain

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