Variant report

Variant	rs12043354
Chromosome Location	chr1:153854424-153854425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153853262..153855003-chr1:154191971..154194003,2	MCF-7	breast:
2	chr1:153848462..153850592-chr1:153853019..153855568,2	MCF-7	breast:
3	chr1:153854243..153856118-chr1:153863285..153864984,2	MCF-7	breast:
4	chr1:153848173..153850836-chr1:153853449..153856009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction

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

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

rs_ID	r²[population]
rs11264522	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264824	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1127092	0.80[ASN][1000 genomes]
rs12023578	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032520	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039936	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044455	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12045838	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12726350	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33998934	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34579266	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34665499	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34752019	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs35170146	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4309017	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4323749	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804837	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61804838	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61804839	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61805526	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6427298	0.83[ASN][1000 genomes]
rs6427334	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6671009	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs67579382	0.80[ASN][1000 genomes]
rs7527406	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9427246	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:153842400-153859400	Weak transcription	Hela-S3	cervix
5	chr1:153842600-153862400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:153842800-153862800	Weak transcription	Thymus	Thymus
7	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
8	chr1:153846400-153871600	Weak transcription	Lung	lung
9	chr1:153849800-153859200	Weak transcription	Psoas Muscle	Psoas
10	chr1:153850200-153858600	Weak transcription	Dnd41	blood
11	chr1:153850800-153855000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:153850800-153856400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:153851200-153855400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr1:153852200-153856400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:153852400-153856400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:153852600-153855600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:153852800-153854600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:153852800-153854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:153852800-153855000	Enhancers	Left Ventricle	heart
20	chr1:153852800-153855000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:153852800-153855600	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:153852800-153855600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:153852800-153855600	Enhancers	Stomach Mucosa	stomach
24	chr1:153852800-153856200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:153853000-153854800	Enhancers	Right Atrium	heart
26	chr1:153853000-153855000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:153853000-153856000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:153853000-153856000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:153853000-153856000	Enhancers	Fetal Heart	heart
30	chr1:153853000-153856400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:153853200-153854600	Active TSS	Brain Germinal Matrix	brain
32	chr1:153853200-153855000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:153853200-153855000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:153853200-153855600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:153853200-153856000	Enhancers	Small Intestine	intestine
36	chr1:153853400-153854600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:153853400-153854600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:153853400-153854800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr1:153853400-153854800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:153853400-153854800	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr1:153853400-153854800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:153853400-153854800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:153853400-153855000	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr1:153853400-153855000	Enhancers	NHEK	skin
45	chr1:153853400-153855000	Flanking Active TSS	Osteobl	bone
46	chr1:153853400-153855200	Enhancers	Right Ventricle	heart
47	chr1:153853400-153855400	Enhancers	HMEC	breast
48	chr1:153853400-153855600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:153853400-153856000	Enhancers	Duodenum Mucosa	Duodenum
50	chr1:153853400-153856600	Enhancers	K562	blood

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