Variant report

Variant	rs9261274
Chromosome Location	chr6:30030789-30030790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:30030646-30031107	K562	blood:	n/a	n/a
2	SETDB1	chr6:30030715-30031031	U2OS	brain:	n/a	n/a
3	CBX3	chr6:30030268-30030994	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30028084..30030840-chr6:30103303..30105686,3	MCF-7	breast:
2	chr6:30002740..30005205-chr6:30029200..30030838,2	MCF-7	breast:
3	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
4	chr6:30002424..30006428-chr6:30027567..30030890,5	MCF-7	breast:
5	chr6:30012267..30014068-chr6:30030146..30031737,2	K562	blood:

No data

Variant related genes	Relation type
PPP1R11	TF binding region
ZNRD1-AS1	TF binding region
ENSG00000204614	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204618	Chromatin interaction

Extended variants
information (count: 172 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs1048412	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17187210	0.93[AFR][1000 genomes]
rs2074479	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2074480	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2074481	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2074482	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2286405	0.95[AFR][1000 genomes]
rs2301753	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2301754	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2394256	0.95[AFR][1000 genomes]
rs2394257	0.88[AFR][1000 genomes]
rs3734835	0.95[AFR][1000 genomes]
rs3757327	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757329	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757331	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765604	0.95[AFR][1000 genomes]
rs3765606	0.95[AFR][1000 genomes]
rs3869067	0.95[AFR][1000 genomes]
rs3869068	0.95[AFR][1000 genomes]
rs3893530	0.94[AFR][1000 genomes]
rs4448133	0.95[AFR][1000 genomes]
rs6457139	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457140	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457141	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902691	0.92[AFR][1000 genomes]
rs6905157	0.95[AFR][1000 genomes]
rs6910507	0.91[AFR][1000 genomes]
rs6910517	0.93[AFR][1000 genomes]
rs6910898	0.93[AFR][1000 genomes]
rs6911279	0.93[AFR][1000 genomes]
rs6911467	0.95[AFR][1000 genomes]
rs6911634	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911724	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911737	0.93[AFR][1000 genomes]
rs6912080	0.93[AFR][1000 genomes]
rs6912154	0.92[AFR][1000 genomes]
rs6912877	0.86[AFR][1000 genomes]
rs6917477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917603	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6919617	0.95[AFR][1000 genomes]
rs6922640	0.93[AFR][1000 genomes]
rs6926792	0.95[AFR][1000 genomes]
rs6930993	0.93[AFR][1000 genomes]
rs6931776	0.95[AFR][1000 genomes]
rs6941318	0.93[AFR][1000 genomes]
rs7738475	0.95[AFR][1000 genomes]
rs7742417	0.95[AFR][1000 genomes]
rs7742871	0.93[AFR][1000 genomes]
rs7746866	0.95[AFR][1000 genomes]
rs7750514	0.92[AFR][1000 genomes]
rs7751116	0.95[AFR][1000 genomes]
rs7758512	0.95[AFR][1000 genomes]
rs7760299	0.95[AFR][1000 genomes]
rs7761314	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7768179	0.84[AFR][1000 genomes]
rs7769930	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770092	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770557	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886997	0.82[AFR][1000 genomes]
rs9260951	0.91[AFR][1000 genomes]
rs9260959	0.86[AFR][1000 genomes]
rs9260960	0.93[AFR][1000 genomes]
rs9260961	0.93[AFR][1000 genomes]
rs9260963	0.93[AFR][1000 genomes]
rs9260964	0.93[AFR][1000 genomes]
rs9260965	0.93[AFR][1000 genomes]
rs9260966	0.93[AFR][1000 genomes]
rs9260967	0.93[AFR][1000 genomes]
rs9260968	0.93[AFR][1000 genomes]
rs9260970	0.93[AFR][1000 genomes]
rs9260971	0.93[AFR][1000 genomes]
rs9260972	0.93[AFR][1000 genomes]
rs9260974	0.93[AFR][1000 genomes]
rs9260975	0.93[AFR][1000 genomes]
rs9260977	0.93[AFR][1000 genomes]
rs9260978	0.93[AFR][1000 genomes]
rs9260979	0.93[AFR][1000 genomes]
rs9260980	0.92[AFR][1000 genomes]
rs9260982	0.93[AFR][1000 genomes]
rs9260987	0.90[AFR][1000 genomes]
rs9260990	0.91[AFR][1000 genomes]
rs9260994	0.88[AFR][1000 genomes]
rs9260995	0.93[AFR][1000 genomes]
rs9260996	0.93[AFR][1000 genomes]
rs9260999	0.93[AFR][1000 genomes]
rs9261000	0.93[AFR][1000 genomes]
rs9261001	0.92[AFR][1000 genomes]
rs9261003	0.92[AFR][1000 genomes]
rs9261004	0.93[AFR][1000 genomes]
rs9261008	0.90[AFR][1000 genomes]
rs9261009	0.92[AFR][1000 genomes]
rs9261010	0.93[AFR][1000 genomes]
rs9261012	0.90[AFR][1000 genomes]
rs9261013	0.93[AFR][1000 genomes]
rs9261015	0.93[AFR][1000 genomes]
rs9261016	0.93[AFR][1000 genomes]
rs9261020	0.92[AFR][1000 genomes]
rs9261022	0.92[AFR][1000 genomes]
rs9261023	0.92[AFR][1000 genomes]
rs9261024	0.92[AFR][1000 genomes]
rs9261026	0.92[AFR][1000 genomes]
rs9261031	0.93[AFR][1000 genomes]
rs9261033	0.93[AFR][1000 genomes]
rs9261049	0.93[AFR][1000 genomes]
rs9261060	0.91[AFR][1000 genomes]
rs9261074	0.92[AFR][1000 genomes]
rs9261103	0.94[AFR][1000 genomes]
rs9261105	0.95[AFR][1000 genomes]
rs9261110	0.95[AFR][1000 genomes]
rs9261111	0.95[AFR][1000 genomes]
rs9261113	0.94[AFR][1000 genomes]
rs9261115	0.95[AFR][1000 genomes]
rs9261116	0.95[AFR][1000 genomes]
rs9261128	0.95[AFR][1000 genomes]
rs9261129	0.95[AFR][1000 genomes]
rs9261137	0.95[AFR][1000 genomes]
rs9261145	0.95[AFR][1000 genomes]
rs9261149	0.93[AFR][1000 genomes]
rs9261150	0.95[AFR][1000 genomes]
rs9261154	0.94[AFR][1000 genomes]
rs9261162	0.90[AFR][1000 genomes]
rs9261163	0.95[AFR][1000 genomes]
rs9261170	0.95[AFR][1000 genomes]
rs9261174	0.95[AFR][1000 genomes]
rs9261180	0.95[AFR][1000 genomes]
rs9261183	0.93[AFR][1000 genomes]
rs9261185	0.93[AFR][1000 genomes]
rs9261186	0.95[AFR][1000 genomes]
rs9261187	0.95[AFR][1000 genomes]
rs9261188	0.94[AFR][1000 genomes]
rs9261189	0.95[AFR][1000 genomes]
rs9261195	0.95[AFR][1000 genomes]
rs9261198	0.92[AFR][1000 genomes]
rs9261199	0.95[AFR][1000 genomes]
rs9261200	0.95[AFR][1000 genomes]
rs9261201	0.95[AFR][1000 genomes]
rs9261204	0.95[AFR][1000 genomes]
rs9261205	0.95[AFR][1000 genomes]
rs9261206	0.95[AFR][1000 genomes]
rs9261209	0.95[AFR][1000 genomes]
rs9261210	0.95[AFR][1000 genomes]
rs9261216	0.95[AFR][1000 genomes]
rs9261217	0.95[AFR][1000 genomes]
rs9261221	0.95[AFR][1000 genomes]
rs9261222	0.93[AFR][1000 genomes]
rs9261224	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261227	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261243	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261251	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261252	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261256	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261258	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261261	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261262	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261278	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261291	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261292	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261294	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261295	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261297	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261298	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261299	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261300	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261302	0.95[AFR][1000 genomes];0.82[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	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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9261274	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30027600-30031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:30030000-30030800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:30030000-30030800	Enhancers	Gastric	stomach
4	chr6:30030000-30031200	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr6:30030000-30031400	Weak transcription	Small Intestine	intestine
6	chr6:30030000-30033600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:30030000-30034200	Weak transcription	Left Ventricle	heart
8	chr6:30030000-30034200	Weak transcription	Ovary	ovary
9	chr6:30030200-30030800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:30030200-30030800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:30030200-30030800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:30030200-30030800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:30030200-30030800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:30030200-30030800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr6:30030200-30030800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:30030200-30030800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:30030200-30030800	Genic enhancers	Fetal Muscle Leg	muscle
18	chr6:30030200-30030800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:30030200-30030800	Weak transcription	NH-A	brain
20	chr6:30030200-30031000	Enhancers	Primary B cells from cord blood	blood
21	chr6:30030200-30031000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:30030200-30031000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:30030200-30031000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr6:30030200-30031000	Enhancers	Fetal Brain Male	brain
25	chr6:30030200-30031000	Genic enhancers	HSMM	muscle
26	chr6:30030200-30031200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:30030200-30031200	Enhancers	Liver	Liver
28	chr6:30030200-30031600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:30030200-30031600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr6:30030200-30031600	Enhancers	GM12878-XiMat	blood
31	chr6:30030200-30031600	Weak transcription	NHDF-Ad	bronchial
32	chr6:30030200-30031800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:30030200-30031800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr6:30030200-30032000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:30030200-30033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:30030200-30033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:30030200-30033600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:30030200-30033600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:30030200-30033600	Weak transcription	Brain Angular Gyrus	brain
40	chr6:30030200-30033600	Weak transcription	Brain Anterior Caudate	brain
41	chr6:30030200-30033600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:30030200-30033600	Weak transcription	Brain Germinal Matrix	brain
43	chr6:30030200-30033600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:30030200-30033600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:30030200-30033600	Weak transcription	Brain Substantia Nigra	brain
46	chr6:30030200-30033600	Weak transcription	Fetal Heart	heart
47	chr6:30030200-30033600	Weak transcription	Fetal Stomach	stomach
48	chr6:30030200-30033600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:30030200-30033600	Weak transcription	A549	lung
50	chr6:30030200-30033800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links