Variant report

Variant	rs3749057
Chromosome Location	chr2:40326505-40326506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC8A1-1	chr2:40324916-40328505	NONHSAT070272

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12151434	0.81[AMR][1000 genomes]
rs3791998	0.90[ASN][1000 genomes]
rs3792000	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60456982	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7422736	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv962064	chr2:40323393-40328838	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40320000-40326600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr2:40320000-40332200	Enhancers	HSMM	muscle
3	chr2:40320000-40332600	Enhancers	NHDF-Ad	bronchial
4	chr2:40321200-40327600	Weak transcription	Fetal Intestine Large	intestine
5	chr2:40321200-40354600	Weak transcription	Right Ventricle	heart
6	chr2:40321400-40327000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:40322000-40330200	Enhancers	NH-A	brain
8	chr2:40322200-40330200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:40322400-40329600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:40322600-40330200	Weak transcription	Hela-S3	cervix
11	chr2:40322800-40329600	Weak transcription	Fetal Lung	lung
12	chr2:40322800-40350200	Weak transcription	Fetal Brain Male	brain
13	chr2:40323400-40327200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:40323400-40328000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:40323400-40332600	Enhancers	Osteobl	bone
16	chr2:40323600-40330000	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:40324000-40328800	Weak transcription	Ovary	ovary
18	chr2:40324800-40329600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:40324800-40330200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:40325000-40327400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:40325200-40330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:40325200-40330200	Weak transcription	NHEK	skin
23	chr2:40325400-40326800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:40325600-40327400	Weak transcription	HSMMtube	muscle
25	chr2:40325600-40328200	Weak transcription	HMEC	breast
26	chr2:40325800-40326800	Weak transcription	NHLF	lung
27	chr2:40325800-40328000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:40326000-40326600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:40326000-40327000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:40326000-40333600	Enhancers	Fetal Heart	heart
31	chr2:40326400-40326800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:40326400-40327000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr2:40326400-40327800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:40326400-40327800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:40326400-40327800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:40326400-40331000	Enhancers	Dnd41	blood

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