Variant report

Variant	rs435404
Chromosome Location	chr2:40440392-40440393
allele	A/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: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10490209	0.84[CEU][hapmap]
rs107008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1641453	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1641454	0.87[ASN][1000 genomes]
rs17025372	0.82[JPT][hapmap]
rs17025380	0.82[JPT][hapmap]
rs17025588	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2072529	0.82[JPT][hapmap]
rs2540904	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs367596	0.87[ASN][1000 genomes]
rs368577	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs368613	0.86[ASN][1000 genomes]
rs371492	0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs373273	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs376303	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs376535	0.80[CHB][hapmap]
rs381610	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs384673	0.96[ASN][1000 genomes]
rs385341	0.82[JPT][hapmap]
rs386984	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs390145	0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs392953	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs395755	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs395987	0.85[CHB][hapmap]
rs398006	0.86[ASN][1000 genomes]
rs404005	0.82[JPT][hapmap]
rs404214	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs404226	0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs407148	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs408263	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs419125	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs436245	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs447136	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs449383	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs450450	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs473400	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs481800	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs530048	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60592471	0.91[ASN][1000 genomes]
rs62148799	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66950674	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6706969	0.87[ASN][1000 genomes]
rs671010	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6757136	0.85[AMR][1000 genomes];0.80[EUR][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	chr2:40437000-40440400	Weak transcription	Left Ventricle	heart
5	chr2:40437200-40441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:40437200-40453200	Weak transcription	Right Ventricle	heart
7	chr2:40438000-40447200	Weak transcription	Fetal Brain Male	brain
8	chr2:40438800-40440600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:40439400-40441600	Enhancers	Osteobl	bone
10	chr2:40439600-40441600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:40439600-40441600	Enhancers	HSMM	muscle
12	chr2:40439800-40441400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:40439800-40441600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:40439800-40441600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:40439800-40441600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr2:40439800-40441600	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:40439800-40441600	Enhancers	NHLF	lung
18	chr2:40440000-40440600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:40440000-40440600	Genic enhancers	Fetal Heart	heart
20	chr2:40440000-40440800	Enhancers	NH-A	brain
21	chr2:40440000-40441200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:40440000-40441400	Enhancers	Rectal Smooth Muscle	rectum
23	chr2:40440000-40441400	Enhancers	HSMMtube	muscle
24	chr2:40440000-40441600	Enhancers	NHDF-Ad	bronchial
25	chr2:40440200-40441400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:40440200-40441400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:40440200-40442200	Enhancers	Colon Smooth Muscle	Colon

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