Variant report

Variant	rs10180319
Chromosome Location	chr2:151026354-151026355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:151019127..151021972-chr2:151024346..151026624,2	K562	blood:
2	chr2:151024105..151026870-chr2:151120233..151122729,2	MCF-7	breast:
3	chr2:151025085..151027146-chr2:151027265..151029673,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYPD6-3	chr2:151026002-151026455	NONHSAT074918

Variant related genes	Relation type
ENSG00000230645	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10178850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10195216	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157219	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11685263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11687975	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693901	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13405415	0.97[ASN][1000 genomes]
rs1374159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2376607	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28871317	0.99[ASN][1000 genomes]
rs4417736	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4567956	0.99[ASN][1000 genomes]
rs4667375	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667376	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667377	0.97[ASN][1000 genomes]
rs4667379	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708312	0.99[ASN][1000 genomes]
rs6719194	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721152	0.99[ASN][1000 genomes]
rs6727767	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6727863	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6750791	0.99[ASN][1000 genomes]
rs7563665	0.99[ASN][1000 genomes]
rs7601392	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287808	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs954077	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][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	nsv1005441	chr2:150457624-151060247	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv995119	chr2:150556150-151294696	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv469524	chr2:150927500-151076920	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv834412	chr2:151014270-151116638	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv583294	chr2:151022044-151037893	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151021800-151026800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:151022200-151026400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:151022200-151026400	Enhancers	Osteobl	bone
4	chr2:151022600-151026400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:151024000-151026400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:151024000-151026400	Enhancers	NHDF-Ad	bronchial
7	chr2:151024000-151026800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:151024200-151026400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:151024800-151026400	Enhancers	A549	lung
10	chr2:151025200-151026600	Enhancers	Colon Smooth Muscle	Colon
11	chr2:151025400-151026400	Enhancers	Adipose Nuclei	Adipose
12	chr2:151025400-151030600	Weak transcription	HUVEC	blood vessel
13	chr2:151026000-151026400	Enhancers	Pancreas	Pancrea
14	chr2:151026000-151027200	Flanking Active TSS	Liver	Liver
15	chr2:151026000-151027400	Enhancers	Dnd41	blood
16	chr2:151026200-151026400	Enhancers	Rectal Smooth Muscle	rectum

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