Variant report

Variant	rs9261373
Chromosome Location	chr6:30059137-30059138
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:30058912-30060334	HCT-116	colon:	n/a	chr6:30059640-30059650
2	MAX	chr6:30059111-30060374	HCT-116	colon:	n/a	chr6:30059640-30059650

No.	Distal block	Cell Line	Cell type
1	chr6:30041884..30044302-chr6:30056325..30059544,3	MCF-7	breast:
2	chr6:30058142..30060356-chr6:30062997..30064640,2	MCF-7	breast:
3	chr6:30058600..30061539-chr6:30062741..30064895,3	MCF-7	breast:
4	chr6:30054428..30057425-chr6:30058219..30060222,2	MCF-7	breast:
5	chr6:30039555..30048654-chr6:30056865..30065735,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252901	TF binding region
ENSG00000204618	Chromatin interaction
ENSG00000252901	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs1048412	0.96[ASN][1000 genomes]
rs11751554	0.81[AFR][1000 genomes]
rs11968367	0.81[AFR][1000 genomes]
rs11968434	0.81[AFR][1000 genomes]
rs17187210	0.83[ASN][1000 genomes]
rs2074479	0.96[ASN][1000 genomes]
rs2074480	0.96[ASN][1000 genomes]
rs2074481	0.96[ASN][1000 genomes]
rs2074482	0.96[ASN][1000 genomes]
rs2286405	0.89[ASN][1000 genomes]
rs2301753	0.96[ASN][1000 genomes]
rs2301754	0.94[ASN][1000 genomes]
rs2394256	0.89[ASN][1000 genomes]
rs2394257	0.85[ASN][1000 genomes]
rs2394734	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3734835	0.89[ASN][1000 genomes]
rs3765604	0.89[ASN][1000 genomes]
rs3765606	0.89[ASN][1000 genomes]
rs3807034	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807035	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3869067	0.89[ASN][1000 genomes]
rs3869068	0.89[ASN][1000 genomes]
rs3893530	0.89[ASN][1000 genomes]
rs4448133	0.89[ASN][1000 genomes]
rs56066609	0.81[AFR][1000 genomes]
rs60418878	0.81[AFR][1000 genomes]
rs61666432	0.81[AFR][1000 genomes]
rs6902691	0.89[ASN][1000 genomes]
rs6905157	0.87[ASN][1000 genomes]
rs6910507	0.81[ASN][1000 genomes]
rs6910517	0.83[ASN][1000 genomes]
rs6910898	0.83[ASN][1000 genomes]
rs6911279	0.83[ASN][1000 genomes]
rs6911467	0.89[ASN][1000 genomes]
rs6911737	0.83[ASN][1000 genomes]
rs6912080	0.83[ASN][1000 genomes]
rs6912154	0.85[ASN][1000 genomes]
rs6919617	0.89[ASN][1000 genomes]
rs6922640	0.85[ASN][1000 genomes]
rs6926792	0.89[ASN][1000 genomes]
rs6930993	0.83[ASN][1000 genomes]
rs6931776	0.89[ASN][1000 genomes]
rs6941318	0.84[ASN][1000 genomes]
rs73424274	0.81[AFR][1000 genomes]
rs7738475	0.89[ASN][1000 genomes]
rs7742417	0.89[ASN][1000 genomes]
rs7742871	0.89[ASN][1000 genomes]
rs7746866	0.89[ASN][1000 genomes]
rs7750514	0.82[ASN][1000 genomes]
rs7751116	0.89[ASN][1000 genomes]
rs7758512	0.89[ASN][1000 genomes]
rs7760299	0.89[ASN][1000 genomes]
rs7768179	0.82[ASN][1000 genomes]
rs7770520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7770546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7771071	0.81[AFR][1000 genomes]
rs8347	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9260951	0.81[ASN][1000 genomes]
rs9260959	0.82[ASN][1000 genomes]
rs9260960	0.83[ASN][1000 genomes]
rs9260961	0.82[ASN][1000 genomes]
rs9260963	0.83[ASN][1000 genomes]
rs9260964	0.83[ASN][1000 genomes]
rs9260965	0.83[ASN][1000 genomes]
rs9260966	0.83[ASN][1000 genomes]
rs9260967	0.83[ASN][1000 genomes]
rs9260968	0.83[ASN][1000 genomes]
rs9260970	0.83[ASN][1000 genomes]
rs9260971	0.83[ASN][1000 genomes]
rs9260972	0.83[ASN][1000 genomes]
rs9260974	0.83[ASN][1000 genomes]
rs9260975	0.83[ASN][1000 genomes]
rs9260977	0.83[ASN][1000 genomes]
rs9260978	0.83[ASN][1000 genomes]
rs9260979	0.83[ASN][1000 genomes]
rs9260980	0.81[ASN][1000 genomes]
rs9260982	0.83[ASN][1000 genomes]
rs9260987	0.83[ASN][1000 genomes]
rs9260990	0.81[ASN][1000 genomes]
rs9260994	0.83[ASN][1000 genomes]
rs9260995	0.83[ASN][1000 genomes]
rs9260996	0.83[ASN][1000 genomes]
rs9260999	0.81[ASN][1000 genomes]
rs9261000	0.83[ASN][1000 genomes]
rs9261003	0.83[ASN][1000 genomes]
rs9261004	0.83[ASN][1000 genomes]
rs9261008	0.82[ASN][1000 genomes]
rs9261009	0.83[ASN][1000 genomes]
rs9261010	0.83[ASN][1000 genomes]
rs9261013	0.83[ASN][1000 genomes]
rs9261015	0.83[ASN][1000 genomes]
rs9261016	0.83[ASN][1000 genomes]
rs9261020	0.85[ASN][1000 genomes]
rs9261022	0.85[ASN][1000 genomes]
rs9261023	0.85[ASN][1000 genomes]
rs9261024	0.85[ASN][1000 genomes]
rs9261026	0.85[ASN][1000 genomes]
rs9261031	0.84[ASN][1000 genomes]
rs9261033	0.83[ASN][1000 genomes]
rs9261049	0.84[ASN][1000 genomes]
rs9261060	0.85[ASN][1000 genomes]
rs9261074	0.86[ASN][1000 genomes]
rs9261103	0.86[ASN][1000 genomes]
rs9261105	0.89[ASN][1000 genomes]
rs9261110	0.89[ASN][1000 genomes]
rs9261111	0.89[ASN][1000 genomes]
rs9261113	0.89[ASN][1000 genomes]
rs9261115	0.89[ASN][1000 genomes]
rs9261116	0.89[ASN][1000 genomes]
rs9261128	0.88[ASN][1000 genomes]
rs9261129	0.89[ASN][1000 genomes]
rs9261137	0.89[ASN][1000 genomes]
rs9261145	0.89[ASN][1000 genomes]
rs9261149	0.89[ASN][1000 genomes]
rs9261150	0.89[ASN][1000 genomes]
rs9261154	0.89[ASN][1000 genomes]
rs9261162	0.89[ASN][1000 genomes]
rs9261163	0.89[ASN][1000 genomes]
rs9261170	0.89[ASN][1000 genomes]
rs9261174	0.89[ASN][1000 genomes]
rs9261180	0.87[ASN][1000 genomes]
rs9261183	0.89[ASN][1000 genomes]
rs9261185	0.89[ASN][1000 genomes]
rs9261186	0.89[ASN][1000 genomes]
rs9261187	0.89[ASN][1000 genomes]
rs9261188	0.89[ASN][1000 genomes]
rs9261189	0.89[ASN][1000 genomes]
rs9261195	0.89[ASN][1000 genomes]
rs9261198	0.89[ASN][1000 genomes]
rs9261199	0.89[ASN][1000 genomes]
rs9261200	0.89[ASN][1000 genomes]
rs9261201	0.87[ASN][1000 genomes]
rs9261204	0.89[ASN][1000 genomes]
rs9261205	0.89[ASN][1000 genomes]
rs9261206	0.87[ASN][1000 genomes]
rs9261209	0.89[ASN][1000 genomes]
rs9261210	0.89[ASN][1000 genomes]
rs9261216	0.89[ASN][1000 genomes]
rs9261217	0.89[ASN][1000 genomes]
rs9261221	0.89[ASN][1000 genomes]
rs9261222	0.89[ASN][1000 genomes]
rs9261291	0.96[ASN][1000 genomes]
rs9261292	0.96[ASN][1000 genomes]
rs9261294	0.96[ASN][1000 genomes]
rs9261295	0.96[ASN][1000 genomes]
rs9261297	0.96[ASN][1000 genomes]
rs9261298	0.96[ASN][1000 genomes]
rs9261299	0.96[ASN][1000 genomes]
rs9261300	0.96[ASN][1000 genomes]
rs9261302	0.96[ASN][1000 genomes]
rs9261306	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261307	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261309	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261310	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261311	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261318	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261366	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261384	0.85[AFR][1000 genomes]
rs9261385	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9261388	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9261389	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs9261373	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30055600-30059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:30056400-30059200	Weak transcription	NHEK	skin
3	chr6:30056400-30059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:30058400-30059600	Bivalent Enhancer	Fetal Thymus	thymus
5	chr6:30058400-30062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:30058600-30060400	Enhancers	NHDF-Ad	bronchial
7	chr6:30058600-30061000	Enhancers	Fetal Intestine Small	intestine
8	chr6:30058600-30061400	Enhancers	Fetal Intestine Large	intestine
9	chr6:30058800-30059400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
10	chr6:30058800-30059400	Enhancers	Hela-S3	cervix
11	chr6:30058800-30059400	Bivalent Enhancer	HepG2	liver
12	chr6:30058800-30059600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:30058800-30059800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:30058800-30060200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:30058800-30060200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:30058800-30060200	Enhancers	Spleen	Spleen
17	chr6:30059000-30059200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr6:30059000-30059400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:30059000-30059600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
20	chr6:30059000-30059800	Bivalent Enhancer	Placenta	Placenta
21	chr6:30059000-30059800	Enhancers	Stomach Mucosa	stomach
22	chr6:30059000-30060000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:30059000-30060000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:30059000-30060200	Enhancers	Esophagus	oesophagus
25	chr6:30059000-30060200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr6:30059000-30060200	Enhancers	HSMM	muscle
27	chr6:30059000-30060200	Enhancers	Osteobl	bone
28	chr6:30059000-30060400	Enhancers	Adipose Nuclei	Adipose

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