Variant report

Variant	rs12729140
Chromosome Location	chr1:212736471-212736472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
2	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
3	chr1:212686720..212688652-chr1:212736381..212737960,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000264590	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10157292	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779581	0.90[CHB][hapmap]
rs10863978	0.86[CHB][hapmap]
rs10863980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863981	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1105899	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11119957	0.86[CHB][hapmap]
rs11119971	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11119972	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11119973	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11119974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119975	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12037048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045591	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12046640	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136405	0.83[ASN][1000 genomes]
rs1877474	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs3806460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951606	0.81[CHB][hapmap]
rs4951609	0.91[CHB][hapmap]
rs4951611	0.91[CHB][hapmap]
rs4951613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951616	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4951618	1.00[CEU][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6671422	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6674072	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs71646170	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212732800-212738000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:212732800-212739600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:212732800-212739600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:212732800-212739800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:212732800-212739800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:212732800-212739800	Weak transcription	Stomach Mucosa	stomach
7	chr1:212732800-212740000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:212733000-212739600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:212733000-212739600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:212733000-212739800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212733000-212739800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:212733000-212740600	Weak transcription	Fetal Heart	heart
13	chr1:212733200-212739600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:212734400-212740000	Weak transcription	Aorta	Aorta
15	chr1:212735000-212739800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:212735200-212738800	Weak transcription	NHLF	lung
17	chr1:212735200-212739800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:212735200-212739800	Weak transcription	Left Ventricle	heart
19	chr1:212735200-212740000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:212735200-212740000	Weak transcription	Right Atrium	heart
21	chr1:212735400-212738400	Weak transcription	HSMMtube	muscle
22	chr1:212735400-212740000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:212735600-212739200	Weak transcription	HUVEC	blood vessel
24	chr1:212735600-212739600	Weak transcription	HSMM	muscle
25	chr1:212735600-212739800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:212735600-212739800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:212735600-212739800	Weak transcription	NH-A	brain
28	chr1:212735800-212739800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:212736000-212738000	Weak transcription	Placenta	Placenta
30	chr1:212736400-212739800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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