Variant report

Variant	rs659042
Chromosome Location	chr11:120997460-120997461
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	chr11:120995573..120997510-chr11:121009843..121012653,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109927	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10892677	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11218161	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12802185	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2186747	0.82[JPT][hapmap]
rs475731	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480761	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583842	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608818	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612969	0.94[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs617692	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633770	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636575	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658494	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524	chr11:120963503-121008167	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs659042	TMEM25	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120975800-121005600	Weak transcription	Right Ventricle	heart
2	chr11:120976600-120998400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:120980600-120998400	Weak transcription	Fetal Brain Female	brain
4	chr11:120991800-120998600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:120992800-120998600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:120993200-121008000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:120993800-121000600	Weak transcription	Fetal Stomach	stomach
8	chr11:120994000-121016200	Weak transcription	Brain Substantia Nigra	brain
9	chr11:120994200-120999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:120994400-121042400	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:120994600-121000600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:120995400-120998600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:120995800-120998400	Weak transcription	Aorta	Aorta
14	chr11:120996400-120998400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:120996400-121005200	Weak transcription	HSMMtube	muscle
16	chr11:120996600-120998400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:120996800-121005400	Weak transcription	Left Ventricle	heart
18	chr11:120996800-121016400	Weak transcription	Ovary	ovary
19	chr11:120996800-121037800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:120997000-120998400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:120997000-120998600	Weak transcription	Fetal Muscle Leg	muscle
22	chr11:120997200-121005000	Weak transcription	Right Atrium	heart

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