Variant report

Variant	rs13029597
Chromosome Location	chr2:86994281-86994282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86992690..86995505-chr2:86996197..86998560,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153561	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10201422	0.84[ASN][1000 genomes]
rs1049457	0.84[ASN][1000 genomes]
rs1049458	0.84[ASN][1000 genomes]
rs11547281	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193	0.84[ASN][1000 genomes]
rs12714203	0.84[ASN][1000 genomes]
rs12997796	0.86[ASN][1000 genomes]
rs13004867	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13297	0.84[ASN][1000 genomes]
rs1850138	0.84[ASN][1000 genomes]
rs2367378	0.84[ASN][1000 genomes]
rs2367379	0.84[ASN][1000 genomes]
rs3020728	0.81[ASN][1000 genomes]
rs34353387	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34933869	0.88[ASN][1000 genomes]
rs35129240	0.88[ASN][1000 genomes]
rs35594332	0.88[ASN][1000 genomes]
rs35815787	0.88[ASN][1000 genomes]
rs4832312	0.84[ASN][1000 genomes]
rs6706378	0.84[ASN][1000 genomes]
rs6711696	0.84[ASN][1000 genomes]
rs6726451	0.84[ASN][1000 genomes]
rs67535255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67856656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67864369	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561172	0.84[ASN][1000 genomes]
rs938486	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv521780	chr2:86974318-86994719	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
17	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86968600-86997600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:86969200-86997800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:86969400-86997800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:86969600-86995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:86969600-86995400	Weak transcription	Esophagus	oesophagus
6	chr2:86970000-87002000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:86970400-86995400	Weak transcription	Aorta	Aorta
8	chr2:86972000-86995400	Weak transcription	Pancreas	Pancrea
9	chr2:86974200-87004200	Weak transcription	Small Intestine	intestine
10	chr2:86974800-86999800	Weak transcription	Stomach Mucosa	stomach
11	chr2:86975400-87003000	Weak transcription	Fetal Brain Male	brain
12	chr2:86975800-86999600	Weak transcription	NHLF	lung
13	chr2:86975800-87006600	Weak transcription	NH-A	brain
14	chr2:86977600-86997800	Weak transcription	HSMMtube	muscle
15	chr2:86977800-86995400	Weak transcription	Fetal Brain Female	brain
16	chr2:86978200-87003000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:86980400-87001400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:86980600-87002800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:86981000-86997000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:86981200-86997600	Weak transcription	HUVEC	blood vessel
21	chr2:86981400-86997000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:86981400-87004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:86981600-87007000	Weak transcription	NHDF-Ad	bronchial
24	chr2:86981800-86995400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:86982000-86999200	Weak transcription	Colonic Mucosa	Colon
26	chr2:86982000-87001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:86982200-86997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:86984200-87006000	Weak transcription	Ovary	ovary
29	chr2:86984600-87007600	Weak transcription	Psoas Muscle	Psoas
30	chr2:86984800-86995400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:86987000-86997400	Weak transcription	Brain Germinal Matrix	brain
32	chr2:86987800-86995400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:86987800-86997600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:86988200-86994600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:86988600-86995000	Weak transcription	Brain Substantia Nigra	brain
36	chr2:86988800-86997400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:86988800-87006200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:86989000-86995000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:86991600-87004600	Strong transcription	Primary B cells from cord blood	blood
40	chr2:86991800-86999600	Strong transcription	HepG2	liver
41	chr2:86991800-87004200	Strong transcription	Primary T cells from cord blood	blood
42	chr2:86991800-87004600	Genic enhancers	Fetal Thymus	thymus
43	chr2:86992000-87003400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:86992200-86998800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:86992200-87003200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:86992200-87004400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:86992200-87004400	Strong transcription	Dnd41	blood
48	chr2:86992200-87004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:86992200-87004600	Strong transcription	Fetal Intestine Large	intestine
50	chr2:86992400-86995400	Weak transcription	Brain Anterior Caudate	brain

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