Variant report

Variant	rs9261260
Chromosome Location	chr6:30023352-30023353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30023200..30024877-chr6:30024886..30026414,2	MCF-7	breast:
2	chr6:30020011..30023371-chr6:30027197..30030746,5	MCF-7	breast:
3	chr6:30014777..30016494-chr6:30021603..30023597,2	K562	blood:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12210298	1.00[ASN][1000 genomes]
rs28400886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260673	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9260679	0.97[EUR][1000 genomes]
rs9260705	0.97[EUR][1000 genomes]
rs9260770	0.97[EUR][1000 genomes]
rs9260802	1.00[EUR][1000 genomes]
rs9260811	1.00[EUR][1000 genomes]
rs9260888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260924	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261267	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261380	1.00[AMR][1000 genomes];1.00[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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv884046	chr6:29997312-30023868	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv981127	chr6:30022896-30023740	Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
5	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
10	chr6:29984600-30023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:29985000-30024600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
13	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
15	chr6:29988400-30023400	Weak transcription	Adipose Nuclei	Adipose
16	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
17	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
20	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:30001200-30025000	Weak transcription	Fetal Lung	lung
22	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
23	chr6:30001800-30024800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:30003000-30027200	Weak transcription	Dnd41	blood
25	chr6:30003200-30024200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:30006200-30027600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:30011000-30027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:30012400-30027400	Weak transcription	HepG2	liver
29	chr6:30012600-30024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:30012600-30024800	Weak transcription	HSMM	muscle
31	chr6:30012600-30027200	Weak transcription	HMEC	breast
32	chr6:30012600-30027800	Weak transcription	Small Intestine	intestine
33	chr6:30012800-30027600	Weak transcription	NHDF-Ad	bronchial
34	chr6:30012800-30027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:30012800-30027800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:30013000-30023800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30013000-30027400	Weak transcription	NHEK	skin
38	chr6:30013000-30027400	Weak transcription	NHLF	lung
39	chr6:30013000-30027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:30013200-30023600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:30013400-30027600	Weak transcription	NH-A	brain
42	chr6:30013600-30027600	Weak transcription	Hela-S3	cervix
43	chr6:30013600-30027800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:30013600-30027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:30013800-30025400	Weak transcription	Psoas Muscle	Psoas
46	chr6:30013800-30027200	Weak transcription	GM12878-XiMat	blood
47	chr6:30014000-30028000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:30015400-30024400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:30015400-30025000	Weak transcription	K562	blood
50	chr6:30015600-30025000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links