Variant report

Variant	rs9261309
Chromosome Location	chr6:30045958-30045959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30045936-30045986	SKMC	muscle:	n/a
2	chr6:30045936-30045986	NHDF-neo	bronchial:	n/a
3	chr6:30045936-30045986	K562	blood:	n/a
4	chr6:30045936-30045986	BE2_C	brain:	n/a
5	chr6:30045936-30045986	HCPEpiC	choroid plexus:	n/a
6	chr6:30045936-30045986	PrEC	prostate:	n/a
7	chr6:30045936-30045986	HUVEC	blood vessel:	n/a
8	chr6:30045936-30045986	SAEC	small airway:	n/a
9	chr6:30045936-30045986	PANC-1	pancreas:	n/a
10	chr6:30045936-30045986	A549	lung:	n/a
11	chr6:30045936-30045986	CMK	blood:	n/a
12	chr6:30045936-30045986	NT2-D1	testis:	n/a
13	chr6:30045936-30045986	Jurkat	blood:	n/a
14	chr6:30045936-30045986	GM12891	blood:	n/a
15	chr6:30045936-30045986	AG09309	skin:	n/a
16	chr6:30045936-30045986	MCF-7	breast:	n/a
17	chr6:30045936-30045986	Hepatocyte	liver:	n/a
18	chr6:30045936-30045986	NHBE	bronchial:	n/a
19	chr6:30045936-30045986	HRCEpiC	kidney:	n/a
20	chr6:30045936-30045986	HEEpiC	esophagus:	n/a
21	chr6:30045936-30045986	AG04449	skin:	fetal
22	chr6:30045936-30045986	GM12892	blood:	n/a
23	chr6:30045936-30045986	SK-N-SH	brain:	n/a
24	chr6:30045936-30045986	HAEpiC	amniotic membrane:	n/a
25	chr6:30045936-30045986	HCT-116	colon:	n/a
26	chr6:30045936-30045986	SK-N-MC	brain:	n/a
27	chr6:30045936-30045986	SK-N-SH_RA	brain:	n/a
28	chr6:30045936-30045986	GM12878	blood:	n/a
29	chr6:30045936-30045986	Caco-2	colon:	n/a
30	chr6:30045936-30045986	T-47D	breast:	n/a
31	chr6:30045936-30045986	HNPCEpiC	eye:	n/a
32	chr6:30045936-30045986	BJ	skin:	n/a
33	chr6:30045936-30045986	IMR90	lung:	fetal
34	chr6:30045936-30045986	MCF10A-Er-Src	breast:	n/a
35	chr6:30045936-30045986	HRPEpiC	eye:	n/a
36	chr6:30045936-30045986	HRE	kidney:	n/a
37	chr6:30045936-30045986	AoSMC	blood vessel:	n/a
38	chr6:30045936-30045986	HPAEpiC	pulmonary alveolar:	n/a
39	chr6:30045936-30045986	HepG2	liver:	n/a
40	chr6:30045936-30045986	AG09319	gingival:	n/a
41	chr6:30045936-30045986	GM19239	blood:	n/a
42	chr6:30045936-30045986	NB4	blood:	n/a
43	chr6:30045936-30045986	HEK293	kidney:	embryo
44	chr6:30045936-30045986	LNCaP	prostate:	n/a
45	chr6:30045936-30045986	U87	brain:	n/a
46	chr6:30045936-30045986	NH-A	brain:	n/a
47	chr6:30045936-30045986	HIPEpiC	eye:	n/a
48	chr6:30045936-30045986	ProgFib	skin:	n/a
49	chr6:30045936-30045986	GM06990	blood:	n/a
50	chr6:30045936-30045986	HL-60	blood:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30044585..30046967-chr6:30097709..30100269,2	MCF-7	breast:
2	chr6:30044892..30047064-chr6:30055499..30057098,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF39	CpG island
ENSG00000252901	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1048412	0.92[ASN][1000 genomes]
rs2074479	0.92[ASN][1000 genomes]
rs2074480	0.92[ASN][1000 genomes]
rs2074481	0.92[ASN][1000 genomes]
rs2074482	0.92[ASN][1000 genomes]
rs2246638	0.83[ASN][1000 genomes]
rs2286405	0.86[ASN][1000 genomes]
rs2301753	0.92[ASN][1000 genomes]
rs2301754	0.90[ASN][1000 genomes]
rs2394256	0.86[ASN][1000 genomes]
rs2394257	0.82[ASN][1000 genomes]
rs2394734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571431	0.80[ASN][1000 genomes]
rs3734835	0.86[ASN][1000 genomes]
rs3765604	0.86[ASN][1000 genomes]
rs3765606	0.86[ASN][1000 genomes]
rs3807034	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3807035	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3869067	0.86[ASN][1000 genomes]
rs3869068	0.86[ASN][1000 genomes]
rs3893530	0.86[ASN][1000 genomes]
rs4448133	0.86[ASN][1000 genomes]
rs6902691	0.86[ASN][1000 genomes]
rs6905157	0.84[ASN][1000 genomes]
rs6911467	0.86[ASN][1000 genomes]
rs6912154	0.82[ASN][1000 genomes]
rs6919617	0.86[ASN][1000 genomes]
rs6922640	0.82[ASN][1000 genomes]
rs6926792	0.86[ASN][1000 genomes]
rs6931776	0.86[ASN][1000 genomes]
rs6941318	0.81[ASN][1000 genomes]
rs7738475	0.86[ASN][1000 genomes]
rs7742417	0.86[ASN][1000 genomes]
rs7742871	0.86[ASN][1000 genomes]
rs7746866	0.86[ASN][1000 genomes]
rs7751116	0.86[ASN][1000 genomes]
rs7758512	0.86[ASN][1000 genomes]
rs7760299	0.86[ASN][1000 genomes]
rs7770520	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7770546	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8347	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261020	0.82[ASN][1000 genomes]
rs9261022	0.82[ASN][1000 genomes]
rs9261023	0.82[ASN][1000 genomes]
rs9261024	0.82[ASN][1000 genomes]
rs9261026	0.82[ASN][1000 genomes]
rs9261031	0.81[ASN][1000 genomes]
rs9261049	0.81[ASN][1000 genomes]
rs9261060	0.82[ASN][1000 genomes]
rs9261074	0.83[ASN][1000 genomes]
rs9261103	0.83[ASN][1000 genomes]
rs9261105	0.86[ASN][1000 genomes]
rs9261110	0.86[ASN][1000 genomes]
rs9261111	0.86[ASN][1000 genomes]
rs9261113	0.86[ASN][1000 genomes]
rs9261115	0.86[ASN][1000 genomes]
rs9261116	0.86[ASN][1000 genomes]
rs9261128	0.85[ASN][1000 genomes]
rs9261129	0.86[ASN][1000 genomes]
rs9261137	0.86[ASN][1000 genomes]
rs9261145	0.86[ASN][1000 genomes]
rs9261149	0.86[ASN][1000 genomes]
rs9261150	0.86[ASN][1000 genomes]
rs9261154	0.86[ASN][1000 genomes]
rs9261162	0.86[ASN][1000 genomes]
rs9261163	0.86[ASN][1000 genomes]
rs9261170	0.86[ASN][1000 genomes]
rs9261174	0.86[ASN][1000 genomes]
rs9261180	0.84[ASN][1000 genomes]
rs9261183	0.86[ASN][1000 genomes]
rs9261185	0.86[ASN][1000 genomes]
rs9261186	0.86[ASN][1000 genomes]
rs9261187	0.86[ASN][1000 genomes]
rs9261188	0.86[ASN][1000 genomes]
rs9261189	0.86[ASN][1000 genomes]
rs9261195	0.86[ASN][1000 genomes]
rs9261198	0.86[ASN][1000 genomes]
rs9261199	0.86[ASN][1000 genomes]
rs9261200	0.86[ASN][1000 genomes]
rs9261201	0.84[ASN][1000 genomes]
rs9261204	0.86[ASN][1000 genomes]
rs9261205	0.86[ASN][1000 genomes]
rs9261206	0.84[ASN][1000 genomes]
rs9261209	0.86[ASN][1000 genomes]
rs9261210	0.86[ASN][1000 genomes]
rs9261216	0.86[ASN][1000 genomes]
rs9261217	0.86[ASN][1000 genomes]
rs9261221	0.86[ASN][1000 genomes]
rs9261222	0.86[ASN][1000 genomes]
rs9261291	0.92[ASN][1000 genomes]
rs9261292	0.92[ASN][1000 genomes]
rs9261294	0.92[ASN][1000 genomes]
rs9261295	0.92[ASN][1000 genomes]
rs9261297	0.92[ASN][1000 genomes]
rs9261298	0.92[ASN][1000 genomes]
rs9261299	0.92[ASN][1000 genomes]
rs9261300	0.92[ASN][1000 genomes]
rs9261302	0.92[ASN][1000 genomes]
rs9261306	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261318	0.83[ASN][1000 genomes]
rs9261366	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9261368	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9261370	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9261371	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9261373	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9261385	0.83[ASN][1000 genomes]
rs9261388	0.83[ASN][1000 genomes]
rs9261389	0.83[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	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
4	nsv884049	chr6:30037353-30047403	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9261309	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30044600-30046600	Bivalent Enhancer	Primary T cells from cord blood	blood
2	chr6:30044800-30046400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:30045200-30046000	Bivalent Enhancer	Fetal Thymus	thymus
4	chr6:30045600-30047000	Enhancers	Dnd41	blood

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