Variant report

Variant	rs55686933
Chromosome Location	chr13:49088327-49088328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49081743..49084542-chr13:49085954..49089235,3	K562	blood:
2	chr13:49088221..49089957-chr13:49104157..49106836,2	MCF-7	breast:
3	chr13:49087919..49090569-chr13:49105572..49108437,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12583617	1.00[EUR][1000 genomes]
rs12583644	1.00[EUR][1000 genomes]
rs12583787	1.00[ASN][1000 genomes]
rs12585384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585742	1.00[EUR][1000 genomes]
rs12857866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071937	1.00[ASN][1000 genomes]
rs2148515	1.00[ASN][1000 genomes]
rs4151472	1.00[EUR][1000 genomes]
rs4151479	1.00[EUR][1000 genomes]
rs4151524	1.00[EUR][1000 genomes]
rs4151598	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151602	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449268	1.00[ASN][1000 genomes]
rs57394470	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650379	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139763	1.00[ASN][1000 genomes]
rs7319276	1.00[ASN][1000 genomes]
rs7326934	1.00[ASN][1000 genomes]
rs73479216	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73479220	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495037	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074944	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074951	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74077638	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316384	1.00[ASN][1000 genomes]
rs9316386	1.00[ASN][1000 genomes]
rs9316387	1.00[ASN][1000 genomes]
rs9316396	1.00[ASN][1000 genomes]
rs9316398	1.00[ASN][1000 genomes]
rs9331984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332055	1.00[ASN][1000 genomes]
rs9332070	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332085	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591176	1.00[ASN][1000 genomes]
rs9595914	1.00[ASN][1000 genomes]
rs9595924	1.00[ASN][1000 genomes]
rs9595926	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	14 gene(s)	inside rSNPs	diseases
5	nsv983709	chr13:49086347-49097905	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
5	chr13:49068000-49105600	Weak transcription	Gastric	stomach
6	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:49071200-49105600	Weak transcription	Fetal Brain Male	brain
8	chr13:49071800-49105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:49072000-49088400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr13:49072200-49095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:49075600-49093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:49075600-49095200	Weak transcription	Fetal Intestine Large	intestine
13	chr13:49075800-49088400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:49075800-49093200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:49076600-49097400	Weak transcription	Pancreas	Pancrea
16	chr13:49079600-49091000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr13:49079600-49092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr13:49080600-49105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:49080800-49102200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr13:49080800-49105400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr13:49081000-49090200	Weak transcription	HSMM	muscle
22	chr13:49081400-49088600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr13:49081400-49105600	Weak transcription	Placenta	Placenta
24	chr13:49083400-49094400	Weak transcription	Fetal Intestine Small	intestine
25	chr13:49083400-49095800	Weak transcription	Spleen	Spleen
26	chr13:49083800-49105600	Weak transcription	Esophagus	oesophagus
27	chr13:49085000-49088400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:49085000-49091200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:49085000-49096000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr13:49085000-49096600	Weak transcription	Small Intestine	intestine
31	chr13:49085000-49104800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:49085000-49104800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr13:49085200-49096000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr13:49085200-49100400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr13:49085200-49105600	Weak transcription	Fetal Thymus	thymus
36	chr13:49085600-49089600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr13:49086200-49088800	Weak transcription	Liver	Liver
38	chr13:49086200-49089200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr13:49086200-49090000	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:49086200-49090400	Weak transcription	Fetal Stomach	stomach
41	chr13:49086200-49090800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:49086200-49091200	Weak transcription	Psoas Muscle	Psoas
43	chr13:49086200-49091200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr13:49086200-49094400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr13:49086200-49102200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr13:49086200-49102400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr13:49086200-49105600	Weak transcription	Lung	lung
48	chr13:49086200-49105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr13:49086200-49105600	Weak transcription	HSMMtube	muscle
50	chr13:49086400-49088400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links