Variant report

Variant	rs2669397
Chromosome Location	chr3:145855446-145855447
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145851329..145855768-chr3:145877369..145881953,7	MCF-7	breast:
2	chr3:145851729..145854083-chr3:145855117..145857839,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11916662	0.86[EUR][1000 genomes]
rs11917712	0.86[EUR][1000 genomes]
rs11917774	0.86[EUR][1000 genomes]
rs11917816	0.86[EUR][1000 genomes]
rs11919826	0.86[EUR][1000 genomes]
rs11925421	0.86[EUR][1000 genomes]
rs12171307	1.00[ASN][1000 genomes]
rs1375579	1.00[ASN][1000 genomes]
rs1375586	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375589	0.85[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512898	0.86[EUR][1000 genomes]
rs1512899	0.86[EUR][1000 genomes]
rs1530742	1.00[ASN][1000 genomes]
rs16857989	0.86[EUR][1000 genomes]
rs1982381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055978	0.86[EUR][1000 genomes]
rs55721145	0.86[EUR][1000 genomes]
rs59713697	0.86[EUR][1000 genomes]
rs6440412	1.00[ASN][1000 genomes]
rs6440418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72989685	0.86[EUR][1000 genomes]
rs72989693	0.86[EUR][1000 genomes]
rs72996210	1.00[EUR][1000 genomes]
rs72996212	1.00[EUR][1000 genomes]
rs73865338	0.86[EUR][1000 genomes]
rs7626859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639115	1.00[ASN][1000 genomes]
rs895928	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830375	1.00[ASN][1000 genomes]
rs9869319	1.00[ASN][1000 genomes]
rs9881770	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
3	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:145843600-145861200	Weak transcription	Right Ventricle	heart
5	chr3:145844600-145856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:145844600-145860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:145848000-145856800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:145850200-145856200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:145850200-145857600	Weak transcription	NHLF	lung
10	chr3:145850400-145860200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:145850400-145864400	Weak transcription	HMEC	breast
12	chr3:145851400-145857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:145851600-145856000	Weak transcription	Ovary	ovary
14	chr3:145851600-145857400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:145851600-145860400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:145851600-145864200	Weak transcription	Right Atrium	heart
17	chr3:145851800-145856800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:145851800-145857600	Weak transcription	HUVEC	blood vessel
19	chr3:145852200-145857600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:145852400-145857800	Weak transcription	Fetal Intestine Large	intestine
21	chr3:145852600-145855800	Weak transcription	Fetal Stomach	stomach
22	chr3:145852600-145856800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:145852600-145857400	Weak transcription	HSMMtube	muscle
24	chr3:145852600-145858000	Weak transcription	Small Intestine	intestine
25	chr3:145852600-145860400	Weak transcription	NH-A	brain
26	chr3:145852800-145855800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:145852800-145856200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:145852800-145856800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:145852800-145856800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:145852800-145856800	Weak transcription	Fetal Lung	lung
31	chr3:145852800-145857200	Weak transcription	NHDF-Ad	bronchial
32	chr3:145852800-145857600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:145852800-145860600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:145853000-145855600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:145853000-145855800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:145853000-145856000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:145853000-145857000	Weak transcription	Liver	Liver
38	chr3:145853000-145857200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:145853000-145857200	Weak transcription	Fetal Kidney	kidney
40	chr3:145853000-145857400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:145853000-145857400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:145853000-145857600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:145853000-145857600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:145853000-145857600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:145853200-145855800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:145853200-145860400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:145853200-145861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:145853400-145855800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:145853400-145857400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:145853600-145856000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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