Variant report

Variant	rs12039936
Chromosome Location	chr1:153854161-153854162
allele	A/G
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	chr1:153848173..153850836-chr1:153853449..153856009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11264522	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1127092	0.80[ASN][1000 genomes]
rs12023578	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032520	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033532	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043354	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044455	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12045838	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12726350	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072704	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297895	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33998934	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34579266	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34665499	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35170146	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4309017	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4323749	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804837	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61804838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61804839	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61805526	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6427298	0.83[ASN][1000 genomes]
rs6427334	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67579382	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7527406	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9427246	0.85[AMR][1000 genomes];0.96[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:153833400-153854400	Weak transcription	Gastric	stomach
5	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:153842400-153859400	Weak transcription	Hela-S3	cervix
7	chr1:153842600-153862400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:153842800-153862800	Weak transcription	Thymus	Thymus
9	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
10	chr1:153846400-153854400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:153846400-153871600	Weak transcription	Lung	lung
12	chr1:153849200-153854400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:153849800-153859200	Weak transcription	Psoas Muscle	Psoas
14	chr1:153850200-153858600	Weak transcription	Dnd41	blood
15	chr1:153850800-153855000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:153850800-153856400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:153851200-153855400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:153852200-153856400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:153852400-153856400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:153852600-153855600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:153852800-153854600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:153852800-153854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:153852800-153855000	Enhancers	Left Ventricle	heart
24	chr1:153852800-153855000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:153852800-153855600	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:153852800-153855600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:153852800-153855600	Enhancers	Stomach Mucosa	stomach
28	chr1:153852800-153856200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:153853000-153854200	Enhancers	Fetal Intestine Large	intestine
30	chr1:153853000-153854200	Enhancers	Fetal Intestine Small	intestine
31	chr1:153853000-153854800	Enhancers	Right Atrium	heart
32	chr1:153853000-153855000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:153853000-153856000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:153853000-153856000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:153853000-153856000	Enhancers	Fetal Heart	heart
36	chr1:153853000-153856400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:153853200-153854200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:153853200-153854200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:153853200-153854200	Flanking Active TSS	Fetal Brain Male	brain
40	chr1:153853200-153854600	Active TSS	Brain Germinal Matrix	brain
41	chr1:153853200-153855000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:153853200-153855000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:153853200-153855600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:153853200-153856000	Enhancers	Small Intestine	intestine
45	chr1:153853400-153854200	Flanking Active TSS	Fetal Lung	lung
46	chr1:153853400-153854400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:153853400-153854400	Enhancers	Primary T cells from cord blood	blood
48	chr1:153853400-153854400	Enhancers	Aorta	Aorta
49	chr1:153853400-153854400	Enhancers	Spleen	Spleen
50	chr1:153853400-153854400	Flanking Active TSS	HSMMtube	muscle

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