Variant report

Variant	rs7329865
Chromosome Location	chr13:49154165-49154166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:49152429-49154926	GM12891	blood:	n/a	n/a
2	RAD21	chr13:49153604-49155108	SK-N-SH	brain:	n/a	chr13:49153823-49153837 chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
3	ZNF384	chr13:49153264-49154849	GM12878	blood:	n/a	n/a
4	SPI1	chr13:49152845-49154231	GM12878	blood:	n/a	chr13:49153582-49153591 chr13:49153486-49153499 chr13:49153487-49153500 chr13:49153493-49153502 chr13:49153489-49153498
5	SMC3	chr13:49152753-49154802	GM12878	blood:	n/a	n/a
6	SMC3	chr13:49153653-49154942	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48806307..48808548-chr13:49152200..49154470,2	MCF-7	breast:
2	chr13:48908843..48909363-chr13:49153698..49154640,2	MCF-7	breast:

Variant related genes	Relation type
LINC00462	TF binding region
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1547660	0.84[ASN][1000 genomes]
rs1926595	0.84[ASN][1000 genomes]
rs1926597	0.84[ASN][1000 genomes]
rs198568	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198571	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198574	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs198575	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198576	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198577	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs198606	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198609	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs198610	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2274400	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs2854362	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs3751380	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs398158	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs403390	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs406098	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4151601	1.00[CEU][hapmap];0.86[CHD][hapmap]
rs425834	0.88[CHB][hapmap]
rs427686	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs61074776	0.84[ASN][1000 genomes]
rs6561448	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6561457	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6561461	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7325962	0.90[JPT][hapmap]
rs7329039	0.84[ASN][1000 genomes]
rs7331851	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7336795	1.00[EUR][1000 genomes]
rs73486867	0.84[ASN][1000 genomes]
rs7985825	0.84[ASN][1000 genomes]
rs7992129	0.84[ASN][1000 genomes]
rs7995216	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7996186	1.00[CEU][hapmap]
rs7996402	0.84[ASN][1000 genomes]
rs7998781	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs8001241	0.88[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs8002565	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9316385	0.83[ASN][1000 genomes]
rs9316401	0.84[ASN][1000 genomes]
rs9331965	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs9331973	1.00[CEU][hapmap]
rs9332054	0.86[CHD][hapmap];0.88[GIH][hapmap]
rs9591172	0.84[ASN][1000 genomes]
rs9591177	0.83[ASN][1000 genomes]
rs9591178	0.84[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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49146800-49157400	Weak transcription	HSMMtube	muscle
3	chr13:49147600-49160800	Weak transcription	Thymus	Thymus
4	chr13:49148400-49158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr13:49148400-49159000	Weak transcription	Pancreas	Pancrea
6	chr13:49148400-49160600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr13:49148800-49157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr13:49150400-49154200	Enhancers	Fetal Thymus	thymus
9	chr13:49150600-49159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr13:49152400-49154200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr13:49152400-49155000	Enhancers	Dnd41	blood
12	chr13:49152600-49154800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:49152600-49155000	Enhancers	Brain Anterior Caudate	brain
14	chr13:49152600-49155400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:49152800-49154200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:49152800-49154400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:49152800-49154400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:49152800-49154400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:49152800-49155000	Enhancers	HepG2	liver
20	chr13:49152800-49155200	Enhancers	Brain Hippocampus Middle	brain
21	chr13:49152800-49155400	Enhancers	HMEC	breast
22	chr13:49153000-49154200	Enhancers	Adipose Nuclei	Adipose
23	chr13:49153000-49154200	Enhancers	Duodenum Mucosa	Duodenum
24	chr13:49153000-49154200	Enhancers	Fetal Intestine Small	intestine
25	chr13:49153000-49154800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr13:49153200-49154400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:49153200-49154600	Enhancers	Primary B cells from peripheral blood	blood
28	chr13:49153200-49154800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr13:49153200-49154800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr13:49153200-49155000	Enhancers	Stomach Mucosa	stomach
31	chr13:49153200-49155200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr13:49153400-49154600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr13:49153400-49154800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr13:49153400-49155000	Enhancers	Brain Cingulate Gyrus	brain
35	chr13:49153400-49158200	Weak transcription	Fetal Lung	lung
36	chr13:49153600-49154200	Enhancers	NHEK	skin
37	chr13:49153600-49154800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:49153600-49154800	Enhancers	Liver	Liver
39	chr13:49153600-49155000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr13:49153800-49154200	Enhancers	Primary T cells from cord blood	blood
41	chr13:49153800-49154200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr13:49153800-49154200	Enhancers	Primary hematopoietic stem cells	blood
43	chr13:49153800-49154200	Enhancers	Fetal Intestine Large	intestine
44	chr13:49153800-49154200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr13:49153800-49154400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:49153800-49154800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:49153800-49154800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:49153800-49154800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr13:49153800-49155000	Enhancers	Brain Substantia Nigra	brain
50	chr13:49154000-49154200	Enhancers	Stomach Smooth Muscle	stomach

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