Variant report

Variant	rs13007579
Chromosome Location	chr2:233725364-233725365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233723958..233726244-chr2:233739412..233742241,2	MCF-7	breast:
2	chr2:233722855..233725653-chr2:233786870..233789525,2	MCF-7	breast:
3	chr2:233723605..233727098-chr2:233736700..233739372,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction

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

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

rs_ID	r²[population]
rs1078323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10933406	0.93[CEU][hapmap]
rs1104764	0.89[CEU][hapmap]
rs11688166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11689851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12105766	0.92[CEU][hapmap]
rs12619195	0.93[CEU][hapmap]
rs12993791	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13001052	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13008436	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13009957	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13021823	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13024330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446309	1.00[CHB][hapmap]
rs17164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1973675	0.92[CEU][hapmap]
rs2289911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2344613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675972	0.85[EUR][1000 genomes]
rs283470	0.93[CEU][hapmap]
rs34707169	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35491427	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4973563	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4973564	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4973569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6704763	0.92[CEU][hapmap]
rs6717048	0.93[CEU][hapmap]
rs6733495	0.93[CEU][hapmap]
rs737027	0.92[CEU][hapmap]
rs7560115	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs778371	0.90[ASN][1000 genomes]
rs921055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs938575	0.83[ASN][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr2:233703400-233726400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:233703400-233726600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:233704400-233726200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:233704400-233726600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:233704600-233726000	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:233704600-233728000	Strong transcription	Primary T cells from cord blood	blood
11	chr2:233704800-233726600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:233705000-233726600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:233705600-233726600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:233705600-233727800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:233712000-233728200	Strong transcription	Fetal Stomach	stomach
16	chr2:233714000-233726400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:233715800-233725400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:233718000-233726400	Strong transcription	Thymus	Thymus
19	chr2:233718000-233726600	Strong transcription	Adipose Nuclei	Adipose
20	chr2:233718200-233726400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:233718200-233726600	Strong transcription	Brain Germinal Matrix	brain
22	chr2:233718400-233726400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:233718600-233726400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:233718600-233727800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:233718600-233727800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:233718800-233726800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:233718800-233727800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:233719200-233726600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:233719800-233726600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr2:233719800-233726600	Strong transcription	Placenta	Placenta
31	chr2:233719800-233726600	Strong transcription	Lung	lung
32	chr2:233719800-233726800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:233720000-233726600	Strong transcription	Rectal Smooth Muscle	rectum
34	chr2:233720000-233727000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:233720200-233726200	Strong transcription	Fetal Brain Female	brain
36	chr2:233720200-233726400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:233720200-233726400	Strong transcription	Brain Hippocampus Middle	brain
38	chr2:233720800-233726600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:233720800-233727800	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:233721200-233726600	Strong transcription	Left Ventricle	heart
41	chr2:233721200-233727800	Strong transcription	Brain Anterior Caudate	brain
42	chr2:233721400-233726600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr2:233721400-233726600	Strong transcription	Fetal Lung	lung
44	chr2:233721400-233727800	Genic enhancers	Fetal Intestine Small	intestine
45	chr2:233721800-233725400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:233721800-233726200	Strong transcription	Osteobl	bone
47	chr2:233722200-233725400	Strong transcription	HSMM	muscle
48	chr2:233722200-233726600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:233722400-233726400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:233722400-233726600	Strong transcription	Rectal Mucosa Donor 31	rectum

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