Variant report

Variant	rs10875943
Chromosome Location	chr12:49676010-49676011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49658709..49660780-chr12:49675611..49677871,3	MCF-7	breast:
2	chr12:49674656..49677388-chr12:49681241..49683027,2	K562	blood:
3	chr12:49674974..49678602-chr12:49682204..49684622,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1QL4-3	chr12:49675882-49676768	ENSG00000250773
2	lnc-C1QL4-3	chr12:49675897-49676768	ENSG00000257960

Variant related genes	Relation type
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11168962	0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs11168963	0.87[CEU][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56222401	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	esv19135	chr12:49676002-49690399	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv558834	chr12:49676010-49691567	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	21743467	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10875943	MCRS1	cis	cerebellum	SCAN
rs10875943	OR10AD1	cis	parietal	SCAN
rs10875943	TMEM117	cis	cerebellum	SCAN
rs10875943	DDN	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49668000-49678000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:49668400-49676200	Weak transcription	NHLF	lung
3	chr12:49668600-49682400	Weak transcription	HMEC	breast
4	chr12:49669000-49676200	Weak transcription	HSMM	muscle
5	chr12:49669000-49676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:49671400-49676200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:49671800-49677600	Weak transcription	Hela-S3	cervix
8	chr12:49672200-49676400	Weak transcription	NHEK	skin
9	chr12:49673400-49676200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr12:49673800-49676200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:49674000-49676200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:49674000-49676200	Weak transcription	A549	lung
13	chr12:49674000-49676600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:49674000-49677600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:49674000-49677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:49674200-49677600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:49675200-49676800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:49675400-49676400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:49675600-49678200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:49675800-49676400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:49675800-49676600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:49675800-49676600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:49675800-49676800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:49676000-49676200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:49676000-49676600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:49676000-49676600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:49676000-49676600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:49676000-49676600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:49676000-49676800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:49676000-49676800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:49676000-49677000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:49676000-49677000	Enhancers	HSMMtube	muscle
33	chr12:49676000-49678200	Enhancers	K562	blood

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