Variant report

Variant	rs10505761
Chromosome Location	chr12:12181599-12181600
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	chr12:12180034..12181901-chr12:12182893..12184952,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1008866	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10505760	0.81[EUR][1000 genomes]
rs10845449	0.91[EUR][1000 genomes]
rs11054605	0.90[EUR][1000 genomes]
rs11054620	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054664	1.00[YRI][hapmap]
rs11054665	1.00[YRI][hapmap]
rs1124833	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12582693	1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs12830229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33910264	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34281024	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34536892	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35279937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35395338	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67444818	0.82[EUR][1000 genomes]
rs7133512	0.91[EUR][1000 genomes]
rs71457113	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71457114	0.81[EUR][1000 genomes]
rs7300879	0.90[EUR][1000 genomes]
rs7312564	0.81[ASN][1000 genomes]
rs7313230	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7486349	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898804	chr12:12058411-12202173	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10505761	LOH12CR1	cis	parietal	SCAN
rs10505761	GPRC5D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12171200-12185400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:12171400-12185200	Weak transcription	Spleen	Spleen
3	chr12:12171800-12185000	Weak transcription	Esophagus	oesophagus
4	chr12:12172200-12184600	Weak transcription	Thymus	Thymus
5	chr12:12175600-12185400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:12178400-12185200	Weak transcription	Small Intestine	intestine
7	chr12:12178400-12185400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:12179000-12181800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:12179000-12184600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:12179000-12184600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:12179000-12184800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:12179000-12184800	Weak transcription	Fetal Thymus	thymus
13	chr12:12179000-12185200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:12179200-12184600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:12179200-12185000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:12180000-12181800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr12:12180400-12181800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:12180400-12185800	Weak transcription	Dnd41	blood
19	chr12:12180600-12181600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:12180800-12183000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:12180800-12185200	Weak transcription	Adipose Nuclei	Adipose
22	chr12:12181400-12181600	Enhancers	GM12878-XiMat	blood

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