Variant report

Variant	rs12817877
Chromosome Location	chr12:30955380-30955381
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	chr12:30949838..30951631-chr12:30954389..30956016,2	K562	blood:
2	chr12:30949301..30951122-chr12:30954767..30957062,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPAN11-2	chr12:30954635-30955645	XLOC_009702
2	lnc-TSPAN11-2	chr12:30954635-30955645	NONHSAT027515

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11051093	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12231427	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12813848	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816259	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12818018	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12819901	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12821717	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12821941	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822194	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828652	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12831234	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12831356	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12831687	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12832973	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12833211	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906802	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34681447	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487941	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6487943	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6487944	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7137488	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7138448	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7296510	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7300659	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301387	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7309444	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7312207	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313984	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314095	0.85[EUR][1000 genomes]
rs7314252	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7314420	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7314518	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314809	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314917	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314922	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7315044	0.82[EUR][1000 genomes]
rs7954753	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7954756	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7954836	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969565	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7975708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975750	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv34091	chr12:30927650-31061815	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv1052957	chr12:30951520-31191197	Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv541439	chr12:30951520-31191197	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1052869	chr12:30951520-31399162	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2422447	chr12:30954811-31449815	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12817877	LINC00941	cis	Nerve Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30950200-30956400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:30950200-30956600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:30950200-30960200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:30950200-30960200	Weak transcription	Pancreas	Pancrea
5	chr12:30950400-30957000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:30950400-30957200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:30950400-30960000	Weak transcription	HUVEC	blood vessel
8	chr12:30950400-30960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:30950400-30960200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:30950400-30960200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:30950800-30955800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:30950800-30957000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:30950800-30957000	Weak transcription	NHEK	skin
14	chr12:30950800-30960200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:30951000-30956400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:30951000-30956600	Strong transcription	NH-A	brain
17	chr12:30951200-30957000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:30951400-30956400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:30951600-30958200	Weak transcription	HSMM	muscle
20	chr12:30952400-30956600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:30952400-30956600	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr12:30952600-30955600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:30952800-30955800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:30953000-30955400	Strong transcription	Osteobl	bone
25	chr12:30953600-30956400	Weak transcription	A549	lung
26	chr12:30953800-30956800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:30954000-30956200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:30954200-30958600	Weak transcription	HMEC	breast
29	chr12:30955000-30957600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:30955000-30959400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr12:30955000-30960200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:30955000-30960200	Weak transcription	Hela-S3	cervix
33	chr12:30955200-30956200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:30955200-30960200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:30955200-30960200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:30955200-30960200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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