Variant report

Variant	rs34681447
Chromosome Location	chr12:30952407-30952408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:43)

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];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816259	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12817877	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.92[EUR][1000 genomes]
rs12831687	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12832973	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12833211	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906802	0.84[AMR][1000 genomes];0.93[EUR][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]
rs7137594	0.80[EUR][1000 genomes]
rs7138448	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7296510	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7300659	1.00[AMR][1000 genomes];0.99[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	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313984	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314095	0.86[EUR][1000 genomes]
rs7314252	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7314420	0.84[AMR][1000 genomes];0.93[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969565	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7975708	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975750	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34681447	LINC00941	cis	Nerve Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30950200-30954600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:30950200-30956400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:30950200-30956600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:30950200-30960200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:30950200-30960200	Weak transcription	Pancreas	Pancrea
6	chr12:30950400-30952600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:30950400-30952800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:30950400-30952800	Weak transcription	A549	lung
9	chr12:30950400-30953000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:30950400-30953000	Weak transcription	HMEC	breast
11	chr12:30950400-30954600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:30950400-30954600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:30950400-30957000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:30950400-30957200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:30950400-30960000	Weak transcription	HUVEC	blood vessel
16	chr12:30950400-30960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:30950400-30960200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:30950400-30960200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:30950800-30952600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:30950800-30954600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:30950800-30955800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:30950800-30957000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:30950800-30957000	Weak transcription	NHEK	skin
24	chr12:30950800-30960200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:30951000-30956400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:30951000-30956600	Strong transcription	NH-A	brain
27	chr12:30951200-30953800	Strong transcription	Hela-S3	cervix
28	chr12:30951200-30957000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:30951400-30955200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:30951400-30956400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:30951600-30958200	Weak transcription	HSMM	muscle
32	chr12:30951800-30952800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:30951800-30953800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr12:30951800-30955200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:30952000-30953000	Weak transcription	Osteobl	bone
36	chr12:30952200-30952800	Enhancers	HepG2	liver
37	chr12:30952400-30956600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:30952400-30956600	Strong transcription	Muscle Satellite Cultured Cells	--

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