Variant report

Variant	rs13210299
Chromosome Location	chr6:36811620-36811621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36808554..36811671-chr6:36814361..36817752,3	MCF-7	breast:
2	chr6:36811002..36813494-chr6:36814165..36817730,3	MCF-7	breast:
3	chr6:36807425..36809491-chr6:36809760..36812415,2	MCF-7	breast:
4	chr6:36811312..36813099-chr6:36818892..36821190,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE5-1	chr6:36811611-36811707	XLOC_005701
2	lnc-CPNE5-1	chr6:36810743-36811911	NONHSAT112234

Variant related genes	Relation type
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11542163	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751310	1.00[ASN][1000 genomes]
rs11751956	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753835	0.82[AMR][1000 genomes]
rs11757851	0.82[AMR][1000 genomes]
rs12660916	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12660989	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191679	1.00[ASN][1000 genomes]
rs13192293	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200132	1.00[ASN][1000 genomes]
rs13205292	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206310	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207209	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552005	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405617	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433592	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510528	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34597881	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869908	1.00[ASN][1000 genomes]
rs34913693	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35819257	0.82[AMR][1000 genomes]
rs36098393	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569352	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569356	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470425	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13210299	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36808600-36818800	Weak transcription	Dnd41	blood
2	chr6:36808800-36816000	Weak transcription	Spleen	Spleen
3	chr6:36808800-36816600	Weak transcription	Aorta	Aorta
4	chr6:36809000-36812200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:36809000-36813800	Enhancers	Fetal Muscle Leg	muscle
6	chr6:36809000-36816600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:36809000-36818600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:36809000-36820200	Weak transcription	Thymus	Thymus
9	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:36809200-36812000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:36809200-36812200	Weak transcription	Brain Germinal Matrix	brain
12	chr6:36809200-36812200	Active TSS	Right Atrium	heart
13	chr6:36809200-36812400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:36809200-36812400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:36809200-36812600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:36809200-36812600	Weak transcription	Fetal Brain Female	brain
17	chr6:36809200-36816000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:36809200-36817000	Weak transcription	Brain Anterior Caudate	brain
19	chr6:36809200-36818000	Weak transcription	HSMM	muscle
20	chr6:36809200-36819200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:36809400-36812000	Weak transcription	HSMMtube	muscle
22	chr6:36809400-36812000	Weak transcription	K562	blood
23	chr6:36809400-36812400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:36809400-36812400	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:36809800-36818400	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:36810000-36813000	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:36810400-36812000	Active TSS	Right Ventricle	heart
28	chr6:36810800-36812400	Enhancers	Psoas Muscle	Psoas
29	chr6:36810800-36813800	Enhancers	Fetal Heart	heart
30	chr6:36811000-36815400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:36811000-36816000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:36811000-36816000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr6:36811200-36814000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:36811200-36815000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:36811400-36811800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:36811400-36813200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:36811400-36823200	Weak transcription	Esophagus	oesophagus
38	chr6:36811600-36811800	Enhancers	Left Ventricle	heart
39	chr6:36811600-36816200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links