Variant report

Variant	rs55727788
Chromosome Location	chr1:70615573-70615574
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70608921..70611354-chr1:70613745..70615584,2	K562	blood:
2	chr1:70613655..70615821-chr1:70616886..70621035,3	K562	blood:
3	chr1:70613655..70616182-chr1:70616886..70621035,4	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489928	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12562802	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12565362	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566666	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131235	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131248	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17131251	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2034756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2210545	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274913	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297484	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297486	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2478801	0.89[AMR][1000 genomes]
rs34821575	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35262515	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767206	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767207	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767208	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767214	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920731	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4649913	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4650031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56902977	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58639674	0.82[ASN][1000 genomes]
rs58696538	0.90[EUR][1000 genomes]
rs58927829	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59234513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60272091	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60441970	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs632517	0.89[AMR][1000 genomes]
rs655588	0.85[AMR][1000 genomes]
rs668525	0.94[AMR][1000 genomes]
rs6702168	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs716240	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74085992	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74085996	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74085999	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74088004	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088016	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74088024	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74088029	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs74088032	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74088035	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088042	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv1796744	chr1:70604106-70621290	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv871339	chr1:70605735-70634463	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55727788	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:70605400-70639400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:70606600-70617600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:70606600-70619600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:70606600-70629600	Weak transcription	Fetal Intestine Small	intestine
8	chr1:70606600-70633800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:70606800-70617000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:70606800-70627800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:70606800-70634800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:70606800-70634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:70607000-70621000	Weak transcription	HSMMtube	muscle
16	chr1:70607000-70622400	Weak transcription	K562	blood
17	chr1:70607000-70629600	Weak transcription	Aorta	Aorta
18	chr1:70607000-70633800	Weak transcription	Brain Germinal Matrix	brain
19	chr1:70607000-70670200	Weak transcription	Psoas Muscle	Psoas
20	chr1:70607000-70670400	Weak transcription	Small Intestine	intestine
21	chr1:70607200-70619200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:70607200-70652600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:70607400-70655200	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:70607800-70629200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:70608000-70626800	Weak transcription	Fetal Stomach	stomach
26	chr1:70608200-70645400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:70608400-70653400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:70608800-70618400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:70608800-70622200	Weak transcription	NHEK	skin
30	chr1:70608800-70654800	Weak transcription	Thymus	Thymus
31	chr1:70608800-70655800	Weak transcription	Esophagus	oesophagus
32	chr1:70609200-70616600	Strong transcription	Liver	Liver
33	chr1:70609200-70633800	Weak transcription	Lung	lung
34	chr1:70609200-70647600	Weak transcription	Colonic Mucosa	Colon
35	chr1:70609200-70650200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:70609400-70628200	Weak transcription	Fetal Brain Female	brain
37	chr1:70609400-70638800	Weak transcription	Placenta	Placenta
38	chr1:70609400-70649800	Weak transcription	Fetal Brain Male	brain
39	chr1:70609600-70618000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:70609600-70623400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:70609600-70625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:70609600-70661200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:70609800-70616600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:70609800-70622200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:70610000-70627200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:70610000-70642600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:70610000-70656600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:70610000-70667800	Weak transcription	HepG2	liver
49	chr1:70610200-70616600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:70610400-70650200	Weak transcription	GM12878-XiMat	blood

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