Variant report

Variant	rs1573958
Chromosome Location	chr2:47302829-47302830
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47212859..47216615-chr2:47301507..47304672,4	MCF-7	breast:
2	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
3	chr2:47299662..47307017-chr2:47401146..47405423,11	MCF-7	breast:
4	chr2:47302688..47305561-chr2:47417562..47420065,2	MCF-7	breast:
5	chr2:47301037..47304852-chr2:47397378..47400468,3	MCF-7	breast:
6	chr2:47302270..47304198-chr2:47307298..47308850,2	MCF-7	breast:
7	chr2:47298364..47306534-chr2:47399903..47404660,8	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1046263	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1046267	1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11125114	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs13393256	1.00[JPT][hapmap]
rs1807327	1.00[JPT][hapmap]
rs1807328	1.00[JPT][hapmap]
rs2570511	0.86[EUR][1000 genomes]
rs2692216	1.00[JPT][hapmap]
rs2692219	1.00[JPT][hapmap]
rs4953458	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6544954	0.94[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7569495	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs940737	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9973596	0.88[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47297000-47303000	Genic enhancers	A549	lung
2	chr2:47297800-47303400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:47297800-47303600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:47298000-47303000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:47298000-47303400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:47298000-47304400	Genic enhancers	Spleen	Spleen
7	chr2:47298800-47303000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:47298800-47303200	Enhancers	Fetal Brain Male	brain
9	chr2:47298800-47305200	Strong transcription	Thymus	Thymus
10	chr2:47299000-47303000	Weak transcription	Hela-S3	cervix
11	chr2:47299000-47303400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:47299200-47304800	Strong transcription	Primary T cells from cord blood	blood
13	chr2:47299200-47306000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:47299400-47303800	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr2:47299600-47303200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:47299600-47303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:47299600-47303200	Genic enhancers	Placenta Amnion	Placenta Amnion
18	chr2:47299800-47303200	Genic enhancers	Fetal Muscle Leg	muscle
19	chr2:47299800-47303600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:47300200-47303600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:47300400-47303000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:47300400-47303800	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:47300600-47304000	Weak transcription	Ovary	ovary
24	chr2:47300600-47310400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:47300800-47304000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:47301000-47303000	Weak transcription	GM12878-XiMat	blood
27	chr2:47301000-47303200	Strong transcription	Fetal Thymus	thymus
28	chr2:47301000-47303400	Weak transcription	Right Atrium	heart
29	chr2:47301000-47303800	Weak transcription	Small Intestine	intestine
30	chr2:47301000-47304600	Enhancers	HSMM	muscle
31	chr2:47301000-47306600	Weak transcription	Brain Germinal Matrix	brain
32	chr2:47301200-47303200	Weak transcription	Pancreas	Pancrea
33	chr2:47301200-47303600	Weak transcription	Aorta	Aorta
34	chr2:47301200-47303600	Weak transcription	NHEK	skin
35	chr2:47301200-47304800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:47301200-47305200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:47301200-47305800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:47301400-47303400	Genic enhancers	Adipose Nuclei	Adipose
39	chr2:47301400-47303600	Weak transcription	Gastric	stomach
40	chr2:47301400-47303800	Weak transcription	Esophagus	oesophagus
41	chr2:47301600-47307200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:47301800-47303600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:47301800-47304200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:47301800-47304600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:47302000-47303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:47302000-47303400	Weak transcription	Fetal Intestine Large	intestine
47	chr2:47302000-47303600	Genic enhancers	Fetal Stomach	stomach
48	chr2:47302000-47303800	Genic enhancers	NHLF	lung
49	chr2:47302000-47304200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr2:47302000-47305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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