Variant report

Variant	rs553948
Chromosome Location	chr6:13364549-13364550
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13364126..13366714-chr6:13711205..13713742,2	MCF-7	breast:
2	chr4:62607481..62608026-chr6:13364428..13365302,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10807431	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10807432	0.86[EUR][1000 genomes]
rs10948650	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12153966	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439536	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2496139	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2496160	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2496161	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2496162	0.89[EUR][1000 genomes]
rs2496173	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28813108	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711978	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474159	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs476904	0.88[EUR][1000 genomes]
rs489396	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491278	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492433	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501987	0.85[EUR][1000 genomes]
rs510932	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs516003	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs517803	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs524118	0.83[EUR][1000 genomes]
rs531256	0.86[EUR][1000 genomes]
rs548119	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs552655	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553671	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs560396	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs564174	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs570315	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573109	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs575709	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs579028	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760579	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7770078	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs821276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821277	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357708	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9367440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13350800-13364600	Weak transcription	Aorta	Aorta
2	chr6:13355600-13383400	Weak transcription	A549	lung
3	chr6:13356200-13364600	Weak transcription	Lung	lung
4	chr6:13356200-13364800	Weak transcription	Colonic Mucosa	Colon
5	chr6:13356200-13365000	Weak transcription	Gastric	stomach
6	chr6:13356200-13367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:13356200-13371800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:13356200-13372000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:13356200-13373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:13356200-13378200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:13356400-13365000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:13356400-13368000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:13357200-13364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:13358000-13364600	Weak transcription	Primary T cells from cord blood	blood
15	chr6:13358000-13364600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:13358000-13364800	Weak transcription	Dnd41	blood
17	chr6:13358000-13371800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:13358200-13364600	Weak transcription	Thymus	Thymus
19	chr6:13358200-13367600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:13358200-13368200	Weak transcription	HMEC	breast
21	chr6:13358400-13367600	Weak transcription	NH-A	brain
22	chr6:13358800-13365000	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:13358800-13365800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr6:13358800-13367400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:13359000-13364600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:13359000-13367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:13359200-13364600	Weak transcription	Brain Anterior Caudate	brain
28	chr6:13359200-13365000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:13359200-13367400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:13359200-13367600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:13359200-13367600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:13359200-13367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:13359400-13364600	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:13359400-13364800	Weak transcription	Brain Substantia Nigra	brain
35	chr6:13359400-13367400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:13359400-13367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:13359800-13364600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:13360600-13365000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:13360800-13364800	Enhancers	Right Atrium	heart
40	chr6:13360800-13370800	Weak transcription	HepG2	liver
41	chr6:13361000-13364600	Weak transcription	Fetal Intestine Small	intestine
42	chr6:13361200-13364600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:13361400-13364600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:13361400-13367400	Weak transcription	HUVEC	blood vessel
45	chr6:13361600-13364600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:13361600-13364800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:13361600-13378200	Weak transcription	Fetal Thymus	thymus
48	chr6:13361800-13364600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:13361800-13364800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:13361800-13364800	Weak transcription	K562	blood

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