Variant report

Variant	rs59517660
Chromosome Location	chr1:9658238-9658239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9648974..9650980-chr1:9658222..9660505,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188807	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12058108	0.96[AFR][1000 genomes]
rs72866302	0.96[AFR][1000 genomes]
rs72867822	1.00[AFR][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	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv871521	chr1:9640291-9666364	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9650000-9661200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:9650400-9676000	Weak transcription	A549	lung
3	chr1:9651400-9672000	Weak transcription	Hela-S3	cervix
4	chr1:9653600-9660000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:9653800-9659400	Weak transcription	Osteobl	bone
6	chr1:9653800-9660400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:9653800-9660400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:9653800-9661000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:9653800-9665000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:9653800-9675400	Weak transcription	Stomach Mucosa	stomach
11	chr1:9653800-9675800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:9654000-9658400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:9654000-9669800	Weak transcription	NHDF-Ad	bronchial
14	chr1:9654000-9672800	Weak transcription	HSMMtube	muscle
15	chr1:9654000-9673200	Weak transcription	NH-A	brain
16	chr1:9654000-9673800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:9654000-9675600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:9654200-9659600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:9654200-9659800	Weak transcription	GM12878-XiMat	blood
20	chr1:9654200-9660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:9654200-9660000	Weak transcription	HSMM	muscle
22	chr1:9654200-9660200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:9654200-9663200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:9654400-9661000	Weak transcription	Fetal Kidney	kidney
25	chr1:9654400-9663000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:9654400-9675400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:9654600-9660000	Weak transcription	NHEK	skin
28	chr1:9654600-9662600	Weak transcription	Fetal Brain Male	brain
29	chr1:9655200-9666600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:9655400-9663800	Strong transcription	Fetal Intestine Small	intestine
31	chr1:9655400-9664800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:9655400-9674200	Strong transcription	Dnd41	blood
33	chr1:9655600-9662200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:9655600-9674200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:9655600-9674600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:9655800-9659000	Strong transcription	Spleen	Spleen
37	chr1:9655800-9663800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:9655800-9664800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:9655800-9665000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr1:9655800-9674000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:9655800-9674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:9655800-9674800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:9656000-9661400	Weak transcription	Psoas Muscle	Psoas
44	chr1:9656000-9674000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:9656200-9659000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:9656200-9659800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:9656200-9663400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:9656200-9663800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:9656400-9664400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:9656400-9664400	Strong transcription	Brain Anterior Caudate	brain

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