Variant report

Variant	rs71439285
Chromosome Location	chr2:40440407-40440408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:40440053..40440830-chr2:40675706..40676650,2	MCF-7	breast:
2	chr2:40440228..40440936-chr2:40471245..40471990,2	MCF-7	breast:
3	chr2:40440009..40440862-chr2:40987001..40987610,3	MCF-7	breast:
4	chr2:40439962..40440629-chr2:40781631..40782440,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-2	chr2:40440309-40440619	ENSG00000227028.2

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13010453	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13015064	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34696712	1.00[AMR][1000 genomes]
rs35108069	1.00[AMR][1000 genomes]
rs71439283	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71439284	1.00[AMR][1000 genomes]
rs71439286	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv526425	chr2:40418386-40447587	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv526074	chr2:40423454-40451724	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40418600-40445800	Weak transcription	Dnd41	blood
3	chr2:40431200-40440600	Weak transcription	Fetal Stomach	stomach
4	chr2:40437200-40441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:40437200-40453200	Weak transcription	Right Ventricle	heart
6	chr2:40438000-40447200	Weak transcription	Fetal Brain Male	brain
7	chr2:40438800-40440600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:40439400-40441600	Enhancers	Osteobl	bone
9	chr2:40439600-40441600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:40439600-40441600	Enhancers	HSMM	muscle
11	chr2:40439800-40441400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:40439800-40441600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:40439800-40441600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:40439800-40441600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:40439800-40441600	Enhancers	Stomach Smooth Muscle	stomach
16	chr2:40439800-40441600	Enhancers	NHLF	lung
17	chr2:40440000-40440600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:40440000-40440600	Genic enhancers	Fetal Heart	heart
19	chr2:40440000-40440800	Enhancers	NH-A	brain
20	chr2:40440000-40441200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:40440000-40441400	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:40440000-40441400	Enhancers	HSMMtube	muscle
23	chr2:40440000-40441600	Enhancers	NHDF-Ad	bronchial
24	chr2:40440200-40441400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:40440200-40441400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:40440200-40442200	Enhancers	Colon Smooth Muscle	Colon
27	chr2:40440400-40441600	Enhancers	Left Ventricle	heart

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