Variant report

Variant	rs59090864
Chromosome Location	chr1:78208789-78208790
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	chr1:78207734..78210591-chr1:78224794..78227087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077254	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1002553	1.00[EUR][1000 genomes]
rs17101054	1.00[EUR][1000 genomes]
rs17101148	1.00[EUR][1000 genomes]
rs35117963	1.00[EUR][1000 genomes]
rs57939520	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59272007	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59814571	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689686	1.00[AMR][1000 genomes]
rs74090629	1.00[AMR][1000 genomes]
rs74090656	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090677	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74090699	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74092307	1.00[AMR][1000 genomes]
rs74092311	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv508326	chr1:78184379-78234247	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78173800-78224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:78182400-78210200	Weak transcription	Psoas Muscle	Psoas
3	chr1:78182800-78210200	Weak transcription	Right Ventricle	heart
4	chr1:78189400-78210200	Weak transcription	NHEK	skin
5	chr1:78190600-78210800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:78191600-78210400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:78191600-78215600	Weak transcription	A549	lung
8	chr1:78192000-78215000	Weak transcription	HSMMtube	muscle
9	chr1:78192200-78222400	Weak transcription	Brain Substantia Nigra	brain
10	chr1:78193000-78221200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:78193600-78222600	Weak transcription	Fetal Kidney	kidney
12	chr1:78194400-78209200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:78194400-78214400	Weak transcription	NHLF	lung
14	chr1:78194400-78223400	Weak transcription	NH-A	brain
15	chr1:78194600-78215200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:78194800-78212600	Weak transcription	Colonic Mucosa	Colon
17	chr1:78195000-78213000	Weak transcription	HepG2	liver
18	chr1:78195200-78210200	Weak transcription	Pancreas	Pancrea
19	chr1:78195200-78210400	Weak transcription	Lung	lung
20	chr1:78195200-78214000	Weak transcription	Small Intestine	intestine
21	chr1:78195400-78213000	Weak transcription	Aorta	Aorta
22	chr1:78195400-78216000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:78195400-78216800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:78195400-78222200	Weak transcription	Gastric	stomach
25	chr1:78195400-78223200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:78195400-78224200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:78195400-78224800	Weak transcription	Spleen	Spleen
28	chr1:78196800-78221800	Weak transcription	Ovary	ovary
29	chr1:78197400-78213200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:78197800-78215000	Weak transcription	Fetal Stomach	stomach
31	chr1:78197800-78221800	Weak transcription	Thymus	Thymus
32	chr1:78197800-78222400	Weak transcription	Fetal Intestine Small	intestine
33	chr1:78197800-78223400	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:78198200-78222200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:78198400-78212200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:78198400-78213000	Weak transcription	Stomach Mucosa	stomach
37	chr1:78198400-78224000	Weak transcription	Esophagus	oesophagus
38	chr1:78200200-78218800	Weak transcription	HUVEC	blood vessel
39	chr1:78202800-78217000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:78203800-78210200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:78204800-78209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:78205000-78210000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:78205200-78210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:78205200-78214600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:78205400-78220200	Weak transcription	GM12878-XiMat	blood
46	chr1:78205400-78221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:78205600-78213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:78205600-78222200	Weak transcription	Fetal Brain Male	brain
49	chr1:78205800-78210200	Weak transcription	HMEC	breast
50	chr1:78205800-78213000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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