Variant report

Variant	rs61812598
Chromosome Location	chr1:154420087-154420088
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	chr1:154377400..154379545-chr1:154419096..154421109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11265613	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12126142	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133641	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12730036	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730935	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753254	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228145	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4129267	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4393147	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4453032	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4537545	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4576655	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845372	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845373	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845620	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845621	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845622	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845623	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56383622	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6664201	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684439	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7512646	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518199	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521458	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7529229	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cerebrospinal fluid levels of Alzheimer's disease-related proteins	25340798	GWAS catalog

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:154408800-154420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:154408800-154420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:154409200-154420600	Weak transcription	Gastric	stomach
11	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
12	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
13	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
14	chr1:154412800-154425800	Weak transcription	HepG2	liver
15	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:154414400-154424400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:154414400-154424400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:154414600-154424400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:154414600-154426000	Weak transcription	Thymus	Thymus
20	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:154415000-154420600	Weak transcription	Pancreas	Pancrea
22	chr1:154415200-154420800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:154415200-154424000	Weak transcription	Fetal Stomach	stomach
24	chr1:154415800-154425800	Weak transcription	Esophagus	oesophagus
25	chr1:154416200-154435800	Strong transcription	Liver	Liver
26	chr1:154416400-154420600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:154416600-154420600	Weak transcription	Spleen	Spleen
28	chr1:154416600-154420800	Weak transcription	Right Ventricle	heart
29	chr1:154416600-154424400	Weak transcription	Colonic Mucosa	Colon
30	chr1:154416600-154425600	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:154416800-154420400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:154417400-154428000	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:154417800-154420400	Weak transcription	Primary T cells from cord blood	blood
34	chr1:154417800-154420600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:154417800-154420600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:154417800-154420600	Weak transcription	Brain Anterior Caudate	brain
37	chr1:154417800-154420600	Weak transcription	HMEC	breast
38	chr1:154417800-154422000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:154417800-154426000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:154418000-154420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:154418000-154420400	Weak transcription	Left Ventricle	heart
42	chr1:154418000-154420400	Weak transcription	Hela-S3	cervix
43	chr1:154418000-154420600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:154418000-154420600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:154418000-154420600	Weak transcription	NHEK	skin
46	chr1:154418000-154425600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:154418000-154425800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:154418000-154428000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
50	chr1:154418200-154425000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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