Variant report

Variant	rs4421592
Chromosome Location	chr1:210338196-210338197
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210336624..210338329-chr1:210405939..210407784,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082497	Chromatin interaction
ENSG00000203706	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1002382	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10746423	0.90[AMR][1000 genomes]
rs10779523	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10779525	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779526	0.92[EUR][1000 genomes]
rs11119425	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119427	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119428	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119429	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12129172	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1334567	0.88[AMR][1000 genomes]
rs1334568	0.89[AMR][1000 genomes]
rs1387933	0.84[AMR][1000 genomes]
rs1413695	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490419	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1933477	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2130630	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs227169	0.86[AMR][1000 genomes]
rs227172	0.88[AMR][1000 genomes]
rs227174	0.84[AMR][1000 genomes]
rs227179	0.84[AMR][1000 genomes]
rs227191	0.81[AMR][1000 genomes]
rs227193	0.81[AMR][1000 genomes]
rs227196	0.81[AMR][1000 genomes]
rs227201	0.83[AMR][1000 genomes]
rs227203	0.83[AMR][1000 genomes]
rs227204	0.87[AMR][1000 genomes]
rs227205	0.87[AMR][1000 genomes]
rs227209	0.91[AMR][1000 genomes]
rs227211	0.87[AMR][1000 genomes]
rs227218	0.81[AMR][1000 genomes]
rs227219	0.81[AMR][1000 genomes]
rs2485890	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2485891	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2485892	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2485893	0.92[EUR][1000 genomes]
rs2485894	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2494168	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2494169	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2494189	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494190	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636376	0.84[AMR][1000 genomes]
rs2743889	0.84[AMR][1000 genomes]
rs4589109	0.82[ASN][1000 genomes]
rs4844508	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4844947	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4844951	0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4844952	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6540580	0.87[AMR][1000 genomes]
rs6540584	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656855	0.88[AMR][1000 genomes]
rs701947	0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs701948	0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap]
rs7519750	0.88[AMR][1000 genomes]
rs7529352	0.83[ASW][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7541569	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs846551	0.81[AMR][1000 genomes]
rs846552	0.81[AMR][1000 genomes]
rs846554	0.82[AMR][1000 genomes]
rs846555	0.82[AMR][1000 genomes]
rs9659395	0.88[AMR][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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv873145	chr1:210302595-210347417	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv468072	chr1:210304319-210338196	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv549104	chr1:210304319-210338196	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv549105	chr1:210304319-210338397	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv873146	chr1:210312760-210347417	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4421592	CR1	cis	parietal	SCAN
rs4421592	DYRK3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210319200-210338400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210329400-210339000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:210333200-210340600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:210337600-210340600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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