Variant report

Variant	rs673677
Chromosome Location	chr6:92400165-92400166
allele	C/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:0)
LncRNA
region (count:2)
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	chr6:92400160-92400210	HCPEpiC	choroid plexus:	n/a
2	chr6:92400160-92400210	HL-60	blood:	n/a
3	chr6:92400160-92400210	HCT-116	colon:	n/a
4	chr6:92400160-92400210	RPTEC	kidney:	n/a
5	chr6:92400160-92400210	HEK293	kidney:	embryo
6	chr6:92400160-92400210	HRCEpiC	kidney:	n/a
7	chr6:92400160-92400210	NHDF-neo	bronchial:	n/a
8	chr6:92400160-92400210	GM19239	blood:	n/a
9	chr6:92400160-92400210	HepG2	liver:	n/a
10	chr6:92400160-92400210	AG10803	skin:	n/a
11	chr6:92400160-92400210	HRE	kidney:	n/a
12	chr6:92400160-92400210	HPAEpiC	pulmonary alveolar:	n/a
13	chr6:92400160-92400210	PANC-1	pancreas:	n/a
14	chr6:92400160-92400210	AG04449	skin:	fetal
15	chr6:92400160-92400210	HCF	heart:	n/a
16	chr6:92400160-92400210	SK-N-MC	brain:	n/a
17	chr6:92400160-92400210	LNCaP	prostate:	n/a
18	chr6:92400160-92400210	GM06990	blood:	n/a
19	chr6:92400160-92400210	HNPCEpiC	eye:	n/a
20	chr6:92400160-92400210	ProgFib	skin:	n/a
21	chr6:92400160-92400210	GM12891	blood:	n/a
22	chr6:92400160-92400210	NHBE	bronchial:	n/a
23	chr6:92400160-92400210	A549	lung:	n/a
24	chr6:92400160-92400210	AG09319	gingival:	n/a
25	chr6:92400160-92400210	ECC-1	luminal epithelium:	n/a
26	chr6:92400160-92400210	HAEpiC	amniotic membrane:	n/a
27	chr6:92400160-92400210	Hepatocyte	liver:	n/a
28	chr6:92400160-92400210	Jurkat	blood:	n/a
29	chr6:92400160-92400210	NH-A	brain:	n/a
30	chr6:92400160-92400210	SK-N-SH	brain:	n/a
31	chr6:92400160-92400210	MCF10A-Er-Src	breast:	n/a
32	chr6:92400160-92400210	HRPEpiC	eye:	n/a
33	chr6:92400160-92400210	GM12892	blood:	n/a
34	chr6:92400160-92400210	K562	blood:	n/a
35	chr6:92400160-92400210	NB4	blood:	n/a
36	chr6:92400160-92400210	AoSMC	blood vessel:	n/a
37	chr6:92400160-92400210	HIPEpiC	eye:	n/a
38	chr6:92400160-92400210	T-47D	breast:	n/a
39	chr6:92400160-92400210	Hela-S3	cervix:	n/a
40	chr6:92400160-92400210	SK-N-SH_RA	brain:	n/a
41	chr6:92400160-92400210	NT2-D1	testis:	n/a
42	chr6:92400160-92400210	BE2_C	brain:	n/a
43	chr6:92400160-92400210	PrEC	prostate:	n/a
44	chr6:92400160-92400210	CMK	blood:	n/a
45	chr6:92400160-92400210	HEEpiC	esophagus:	n/a
46	chr6:92400160-92400210	HUVEC	blood vessel:	n/a
47	chr6:92400160-92400210	SKMC	muscle:	n/a
48	chr6:92400160-92400210	HCM	heart:	n/a
49	chr6:92400160-92400210	ovcar-3	ovarian:	n/a
50	chr6:92400160-92400210	BJ	skin:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP3K7-2	chr6:92400120-92400274	NONHSAT113995
2	lnc-MAP3K7-2	chr6:92400120-92400274	ucscGeneNc_uc003pod_2

No data

Variant related genes	Relation type
CASC6	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1761783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478120	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs478536	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481555	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs482426	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs484288	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484406	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs488091	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs504879	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506122	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs508629	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511077	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512950	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs520631	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524271	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs525943	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533135	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs540315	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs542101	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548810	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567888	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570258	0.85[EUR][1000 genomes]
rs570400	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs571387	0.84[EUR][1000 genomes]
rs574724	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578427	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs583239	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs599553	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs601701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605570	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs605594	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs609383	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614298	0.85[EUR][1000 genomes]
rs615105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633637	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs635450	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636295	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs648475	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs650256	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs650804	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655846	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs658041	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs661782	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs666390	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs676663	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678605	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71556396	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017467	chr6:91802015-92417554	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv538360	chr6:91802015-92417554	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034981	chr6:92280070-92530848	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1018145	chr6:92328392-92951562	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv428491	chr6:92329694-92474678	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1028736	chr6:92362109-92423792	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	nsv1067623	chr6:92383159-92939893	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv531366	chr6:92383159-92939893	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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