Variant report

Variant	rs11746535
Chromosome Location	chr5:40824962-40824963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40797697..40800949-chr5:40824816..40830013,8	MCF-7	breast:
2	chr5:40823890..40825642-chr5:40844270..40847206,2	MCF-7	breast:
3	chr5:40753276..40755081-chr5:40822441..40825001,2	MCF-7	breast:
4	chr5:40753095..40762740-chr5:40824814..40831828,21	K562	blood:
5	chr5:40773648..40776497-chr5:40822684..40825519,3	K562	blood:
6	chr5:40812798..40819830-chr5:40821906..40830676,11	MCF-7	breast:
7	chr5:40765162..40773094-chr5:40824590..40832435,13	K562	blood:

Variant related genes	Relation type
ENSG00000132356	Chromatin interaction
ENSG00000113638	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10064650	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1070444	0.93[EUR][1000 genomes]
rs11743132	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743196	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748087	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748743	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749955	1.00[ASN][1000 genomes]
rs12186450	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188981	0.81[EUR][1000 genomes]
rs62357568	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357569	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357570	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357571	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357574	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62357600	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704034	0.92[EUR][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	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
3	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40808400-40826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:40808800-40825600	Weak transcription	HSMM	muscle
3	chr5:40814200-40826000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:40814200-40826000	Weak transcription	GM12878-XiMat	blood
5	chr5:40814200-40826400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:40814400-40825000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:40814400-40825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:40814600-40827000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:40816600-40826600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:40816600-40826800	Weak transcription	Brain Angular Gyrus	brain
11	chr5:40818600-40826600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:40818600-40827000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:40818800-40825200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:40818800-40826200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:40819000-40825200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:40819000-40825600	Weak transcription	NH-A	brain
17	chr5:40819000-40825600	Weak transcription	NHLF	lung
18	chr5:40819400-40826600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:40819600-40826600	Weak transcription	Primary B cells from cord blood	blood
20	chr5:40820000-40826400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr5:40820000-40826600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:40820000-40826800	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:40820200-40825600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:40820400-40825600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:40820400-40827400	Weak transcription	Brain Substantia Nigra	brain
26	chr5:40820800-40825200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:40820800-40825400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:40821000-40827400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:40821200-40825600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:40821400-40825400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:40821400-40828800	Weak transcription	Gastric	stomach
32	chr5:40821600-40825600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:40821600-40825600	Weak transcription	Fetal Stomach	stomach
34	chr5:40821600-40827200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:40821800-40825200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:40822000-40826800	Weak transcription	Esophagus	oesophagus
37	chr5:40822200-40825400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:40822200-40825600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:40822200-40825600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:40822200-40825600	Weak transcription	Spleen	Spleen
41	chr5:40822400-40826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:40822400-40826800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:40822600-40825200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:40822600-40826000	Weak transcription	Fetal Brain Female	brain
45	chr5:40823000-40826400	Weak transcription	Small Intestine	intestine
46	chr5:40823400-40825000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:40823400-40825400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:40823600-40825000	Enhancers	K562	blood
49	chr5:40823600-40825200	Weak transcription	Liver	Liver
50	chr5:40823600-40825200	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links