Variant report

Variant	rs12711782
Chromosome Location	chr2:114457362-114457363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RABL2A-5	chr2:114457238-114457575	l_1932_chr2:114450946-114476823_testes

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11678202	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11888457	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889819	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711783	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13393663	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709158	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6726001	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7561042	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12711782	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs12711782	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114444200-114459200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:114448800-114459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:114451600-114461400	Weak transcription	Esophagus	oesophagus
4	chr2:114451600-114461800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:114451600-114462400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:114451800-114457600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:114452000-114457600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:114452000-114457800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:114452200-114457400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:114452200-114457600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:114452400-114457400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:114452400-114457800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:114452400-114470200	Weak transcription	Primary T cells from cord blood	blood
14	chr2:114452600-114457600	Weak transcription	Thymus	Thymus
15	chr2:114452600-114461200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:114452600-114469400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:114452800-114457400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:114452800-114457800	Weak transcription	Dnd41	blood
19	chr2:114453000-114470400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:114455000-114470400	Weak transcription	NHEK	skin
21	chr2:114455400-114472200	Weak transcription	HMEC	breast
22	chr2:114455600-114470400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:114455800-114462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:114455800-114470400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:114456400-114458400	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:114456600-114457600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr2:114456600-114457600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:114456600-114458200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:114456600-114458200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr2:114456600-114458200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:114456800-114458000	Enhancers	Primary B cells from cord blood	blood
32	chr2:114456800-114458200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:114456800-114458200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:114456800-114458200	Enhancers	HepG2	liver
35	chr2:114456800-114458400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:114457000-114457600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:114457200-114457400	Enhancers	Spleen	Spleen
38	chr2:114457200-114457600	Active TSS	GM12878-XiMat	blood
39	chr2:114457200-114458200	Enhancers	Primary T cells fromperipheralblood	blood

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