Variant report

Variant	rs2595242
Chromosome Location	chr3:158991930-158991931
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	chr3:158991788..158993700-chr3:158997368..159000280,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12635142	0.87[CHB][hapmap]
rs13074822	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs1375403	0.83[CHB][hapmap]
rs1375405	0.83[CHB][hapmap]
rs1375407	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1448998	0.83[CHB][hapmap]
rs1449012	0.83[CHB][hapmap]
rs1449024	0.83[CHB][hapmap]
rs1449027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1562671	0.83[CHB][hapmap]
rs1562672	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17795566	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1900861	0.82[CHB][hapmap]
rs1975601	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2084507	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap]
rs2365478	0.91[CHB][hapmap]
rs2595232	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2595236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2595238	0.95[ASN][1000 genomes]
rs2595239	0.93[ASN][1000 genomes]
rs2595240	0.93[YRI][hapmap]
rs2595243	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2595244	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs2595245	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2595246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs2595247	0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2595248	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2595250	0.93[ASN][1000 genomes]
rs2595258	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs2621277	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs2621282	1.00[ASN][1000 genomes]
rs2621284	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2621285	0.92[YRI][hapmap]
rs2621286	0.93[YRI][hapmap]
rs2621290	0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2621292	0.87[CHB][hapmap]
rs2621294	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2621295	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2621297	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs2621299	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2621300	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2621303	0.93[YRI][hapmap]
rs2621306	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2621310	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2621312	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs2621313	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2621314	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs35192832	0.96[ASN][1000 genomes]
rs4645169	0.91[CHB][hapmap]
rs4680494	0.90[CHB][hapmap]
rs4680495	0.91[CHB][hapmap]
rs4680500	0.83[CHB][hapmap]
rs6441255	0.83[CHB][hapmap]
rs6787941	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap]
rs6789496	0.82[CHB][hapmap]
rs6807076	0.83[CHB][hapmap]
rs73166218	0.92[ASN][1000 genomes]
rs7428369	0.83[CHB][hapmap]
rs7634829	0.82[CHB][hapmap]
rs7646959	0.83[CHB][hapmap]
rs9855265	0.85[CEU][hapmap]
rs9879667	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2595242	IQCJ	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158990600-158992200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr3:158991200-158992000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:158991200-158995400	Active TSS	Fetal Brain Female	brain
4	chr3:158991400-158992000	Active TSS	Brain Hippocampus Middle	brain
5	chr3:158991800-158992800	Weak transcription	Brain Angular Gyrus	brain

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