Variant report

Variant	rs11119972
Chromosome Location	chr1:212733925-212733926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
2	chr1:212670746..212672683-chr1:212733125..212734851,2	K562	blood:
3	chr1:212650902..212653623-chr1:212731690..212733930,2	K562	blood:
4	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
5	chr1:212702412..212705298-chr1:212732068..212734031,2	K562	blood:
6	chr1:212717692..212719261-chr1:212731770..212733992,2	K562	blood:
7	chr1:212717692..212719573-chr1:212732031..212733992,2	K562	blood:
8	chr1:212674417..212676345-chr1:212732607..212734870,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATF3-1	chr1:212733389-212734165	XLOC_000555

No data

Variant related genes	Relation type
ENSG00000264590	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000228067	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10157292	0.91[ASN][1000 genomes]
rs10779581	0.95[CHB][hapmap]
rs10863978	0.90[CHB][hapmap]
rs10863979	0.80[ASN][1000 genomes]
rs10863980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10863981	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1105899	0.83[CHD][hapmap];0.87[JPT][hapmap]
rs11119957	0.91[CHB][hapmap]
rs11119970	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11119971	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11119973	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11119974	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11119975	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11119977	1.00[JPT][hapmap]
rs12037048	0.90[ASN][1000 genomes]
rs12038766	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12041940	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12046640	0.90[ASN][1000 genomes]
rs12136405	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12729140	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1877474	0.93[JPT][hapmap]
rs2884515	0.89[YRI][hapmap]
rs3806460	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4951453	0.80[AMR][1000 genomes]
rs4951606	0.85[CHB][hapmap]
rs4951609	0.95[CHB][hapmap]
rs4951611	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4951613	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4951618	0.86[JPT][hapmap]
rs502502	0.84[JPT][hapmap]
rs606996	0.80[AMR][1000 genomes]
rs6674072	0.93[JPT][hapmap]
rs7553505	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs791561	0.80[AMR][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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212732400-212734800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:212732400-212734800	Weak transcription	Lung	lung
3	chr1:212732400-212734800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:212732400-212736000	Enhancers	Placenta	Placenta
5	chr1:212732600-212734400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:212732600-212734600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:212732800-212734200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:212732800-212734200	Weak transcription	HSMMtube	muscle
9	chr1:212732800-212734200	Weak transcription	NH-A	brain
10	chr1:212732800-212734200	Weak transcription	NHDF-Ad	bronchial
11	chr1:212732800-212734400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:212732800-212734400	Weak transcription	HSMM	muscle
13	chr1:212732800-212734400	Weak transcription	HUVEC	blood vessel
14	chr1:212732800-212734600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:212732800-212734600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:212732800-212734600	Enhancers	Hela-S3	cervix
17	chr1:212732800-212734800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:212732800-212734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:212732800-212734800	Weak transcription	Left Ventricle	heart
20	chr1:212732800-212734800	Weak transcription	Right Atrium	heart
21	chr1:212732800-212735000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:212732800-212735000	Weak transcription	HMEC	breast
23	chr1:212732800-212738000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:212732800-212739600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212732800-212739600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:212732800-212739800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:212732800-212739800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:212732800-212739800	Weak transcription	Stomach Mucosa	stomach
29	chr1:212732800-212740000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:212733000-212734400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:212733000-212734400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:212733000-212734400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:212733000-212734400	Weak transcription	NHLF	lung
34	chr1:212733000-212734400	Weak transcription	Osteobl	bone
35	chr1:212733000-212734600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:212733000-212734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:212733000-212734600	Weak transcription	A549	lung
38	chr1:212733000-212734800	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:212733000-212734800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:212733000-212735000	Weak transcription	NHEK	skin
41	chr1:212733000-212739600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:212733000-212739600	Weak transcription	Adipose Nuclei	Adipose
43	chr1:212733000-212739800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:212733000-212739800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:212733000-212740600	Weak transcription	Fetal Heart	heart
46	chr1:212733200-212734200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:212733200-212734400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:212733200-212739600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:212733400-212735000	Weak transcription	K562	blood
50	chr1:212733800-212734200	Weak transcription	Aorta	Aorta

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