Variant report

Variant	rs11753720
Chromosome Location	chr6:13400406-13400407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13400278..13401808-chr6:13406310..13408265,2	MCF-7	breast:
2	chr6:13397740..13400586-chr6:13613823..13615794,2	K562	blood:

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10807437	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11754291	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758233	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1837701	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119483	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327673	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4145562	0.81[EUR][1000 genomes]
rs487607	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488885	0.80[ASN][1000 genomes]
rs494026	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs500197	0.89[ASN][1000 genomes]
rs513613	0.89[ASN][1000 genomes]
rs520828	0.83[ASN][1000 genomes]
rs523221	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536916	0.89[ASN][1000 genomes]
rs536998	0.89[ASN][1000 genomes]
rs559612	0.83[ASN][1000 genomes]
rs563662	0.89[ASN][1000 genomes]
rs565013	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385763	0.81[EUR][1000 genomes]
rs62386724	0.83[ASN][1000 genomes]
rs62386725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386727	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742086	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs821298	0.89[ASN][1000 genomes]
rs821300	0.89[ASN][1000 genomes]
rs9296672	0.81[EUR][1000 genomes]
rs935061	0.81[EUR][1000 genomes]
rs9357720	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463764	0.81[EUR][1000 genomes]
rs9474117	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13395600-13402800	Enhancers	Fetal Heart	heart
3	chr6:13396000-13404400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:13396200-13407000	Weak transcription	Gastric	stomach
5	chr6:13396400-13404400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:13396600-13405800	Weak transcription	HepG2	liver
7	chr6:13396800-13404400	Weak transcription	NHLF	lung
8	chr6:13397000-13404600	Weak transcription	Aorta	Aorta
9	chr6:13398000-13404400	Weak transcription	Esophagus	oesophagus
10	chr6:13398000-13404600	Weak transcription	Small Intestine	intestine
11	chr6:13398000-13406000	Weak transcription	Lung	lung
12	chr6:13398200-13406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:13398400-13400600	Enhancers	Stomach Smooth Muscle	stomach
14	chr6:13398400-13400600	Enhancers	GM12878-XiMat	blood
15	chr6:13398400-13400600	Weak transcription	K562	blood
16	chr6:13398400-13400800	Weak transcription	HUVEC	blood vessel
17	chr6:13398400-13407400	Weak transcription	Placenta	Placenta
18	chr6:13398600-13406000	Weak transcription	Primary B cells from cord blood	blood
19	chr6:13399000-13401000	Weak transcription	HMEC	breast
20	chr6:13399000-13404400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:13399000-13404400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:13399000-13404600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:13399000-13404800	Weak transcription	Spleen	Spleen
24	chr6:13399200-13401200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:13399200-13401600	Enhancers	Right Atrium	heart
26	chr6:13399200-13403600	Weak transcription	Hela-S3	cervix
27	chr6:13399200-13404000	Weak transcription	Brain Angular Gyrus	brain
28	chr6:13399200-13404000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:13399200-13404400	Weak transcription	Adipose Nuclei	Adipose
30	chr6:13399200-13404400	Weak transcription	Psoas Muscle	Psoas
31	chr6:13399200-13404400	Weak transcription	A549	lung
32	chr6:13399200-13404600	Weak transcription	HSMMtube	muscle
33	chr6:13399200-13406800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:13399400-13400800	Weak transcription	Right Ventricle	heart
35	chr6:13399400-13401000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:13399400-13401200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:13399400-13404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:13399400-13404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:13399400-13404400	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:13399400-13404400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:13399400-13404400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:13399400-13404400	Weak transcription	NHEK	skin
43	chr6:13399400-13404600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr6:13399400-13405800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:13399600-13400600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:13399800-13404400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:13400000-13401000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:13400000-13403200	Weak transcription	NH-A	brain
49	chr6:13400000-13404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:13400200-13401600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links