Variant report

Variant	rs1842156
Chromosome Location	chr3:133122216-133122217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133116761..133118281-chr3:133121220..133123369,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10512891	0.89[CEU][hapmap]
rs10512896	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1197316	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13072106	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13091006	0.81[ASN][1000 genomes]
rs13097026	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1513372	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs16840161	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs16840309	0.86[GIH][hapmap]
rs16840382	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs1708373	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs17297332	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1849505	0.81[ASN][1000 genomes]
rs1920021	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2137602	0.81[ASN][1000 genomes]
rs33998360	0.81[ASN][1000 genomes]
rs34066880	0.81[ASN][1000 genomes]
rs34391675	0.81[ASN][1000 genomes]
rs35128664	0.81[ASN][1000 genomes]
rs35147454	0.81[ASN][1000 genomes]
rs35186564	0.81[ASN][1000 genomes]
rs35356925	0.81[ASN][1000 genomes]
rs35785369	0.81[ASN][1000 genomes]
rs67196950	0.81[ASN][1000 genomes]
rs67607639	0.81[ASN][1000 genomes]
rs71315696	0.81[ASN][1000 genomes]
rs71315702	0.81[ASN][1000 genomes]
rs73207714	0.81[ASN][1000 genomes]
rs73863529	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612595	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7625110	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7650741	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460857	chr3:133101390-133122216	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv591801	chr3:133101390-133122216	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877504	chr3:133122216-133172374	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1842156	C3orf36	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133099600-133122600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:133103400-133123200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:133103400-133123600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:133103800-133123800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:133104400-133131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:133107200-133123800	Weak transcription	Fetal Thymus	thymus
7	chr3:133110800-133123600	Weak transcription	HSMM	muscle
8	chr3:133113600-133123600	Weak transcription	HSMMtube	muscle
9	chr3:133114200-133127400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:133120800-133123600	Weak transcription	Fetal Brain Female	brain
11	chr3:133121000-133123600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:133121200-133122600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:133121600-133124800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:133121800-133122800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:133122000-133122400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr3:133122000-133124000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:133122000-133124200	Enhancers	Brain Hippocampus Middle	brain
18	chr3:133122000-133124600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:133122200-133122800	Enhancers	Fetal Lung	lung
20	chr3:133122200-133123000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:133122200-133123000	Enhancers	Brain Angular Gyrus	brain
22	chr3:133122200-133123800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:133122200-133124000	Enhancers	Brain Substantia Nigra	brain
24	chr3:133122200-133124000	Enhancers	Fetal Muscle Leg	muscle
25	chr3:133122200-133124200	Enhancers	Brain Cingulate Gyrus	brain
26	chr3:133122200-133124200	Enhancers	Brain Inferior Temporal Lobe	brain

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