Variant report

Variant	rs17030592
Chromosome Location	chr1:113174107-113174108
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113160723..113165186-chr1:113170921..113177730,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10399919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102490	0.80[YRI][hapmap];0.90[AFR][1000 genomes]
rs11102500	0.90[AFR][1000 genomes]
rs11102519	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060267	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069022	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs12069740	0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073750	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077330	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080006	0.90[AFR][1000 genomes]
rs12082350	0.83[AFR][1000 genomes]
rs12087862	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091635	0.90[AFR][1000 genomes]
rs12094504	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs12095563	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030446	0.83[AFR][1000 genomes]
rs17030451	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs17030455	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs17030475	0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs4424506	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57573777	1.00[AMR][1000 genomes]
rs58634778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59053530	1.00[AMR][1000 genomes]
rs59324334	0.85[AFR][1000 genomes]
rs61203550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984509	1.00[AMR][1000 genomes]
rs72984515	1.00[AMR][1000 genomes]
rs72986505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72986535	1.00[AMR][1000 genomes]
rs72993072	0.90[AFR][1000 genomes]
rs9919308	0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription 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 miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
6	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163600-113180600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
3	chr1:113163800-113176000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:113164200-113175800	Weak transcription	Fetal Brain Female	brain
8	chr1:113164200-113180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
10	chr1:113164800-113179200	Weak transcription	Colonic Mucosa	Colon
11	chr1:113165400-113174400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:113165400-113175200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:113165400-113176400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:113165600-113174400	Genic enhancers	K562	blood
15	chr1:113167800-113176200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:113168000-113180000	Weak transcription	Aorta	Aorta
17	chr1:113168600-113177800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:113168600-113179200	Weak transcription	NH-A	brain
19	chr1:113168800-113174800	Weak transcription	Right Atrium	heart
20	chr1:113168800-113177600	Weak transcription	Stomach Mucosa	stomach
21	chr1:113168800-113177800	Weak transcription	NHLF	lung
22	chr1:113168800-113178200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:113168800-113179200	Weak transcription	Brain Angular Gyrus	brain
24	chr1:113168800-113179200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:113168800-113179200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:113168800-113179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:113168800-113180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:113168800-113180000	Weak transcription	Lung	lung
29	chr1:113168800-113187200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:113168800-113189800	Weak transcription	Fetal Lung	lung
31	chr1:113168800-113191000	Weak transcription	Ovary	ovary
32	chr1:113168800-113199800	Weak transcription	Esophagus	oesophagus
33	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
34	chr1:113169000-113181600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:113169000-113186400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:113169000-113189800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:113169200-113174800	Weak transcription	Gastric	stomach
38	chr1:113169200-113188400	Weak transcription	Left Ventricle	heart
39	chr1:113169800-113176600	Weak transcription	A549	lung
40	chr1:113169800-113178600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:113169800-113188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:113170000-113174800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:113170000-113179200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:113171200-113175000	Strong transcription	Primary T cells from cord blood	blood
45	chr1:113171400-113174800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:113171400-113175800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:113171400-113176200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:113171600-113174200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:113171600-113174600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:113171600-113175000	Strong transcription	Dnd41	blood

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