Variant report

Variant	rs3117194
Chromosome Location	chr6:29426008-29426009
allele	C/T
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: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	chr6:29425960-29426010	HAEpiC	amniotic membrane:	n/a
2	chr6:29425960-29426010	H1-hESC	embryonic stem cell:	embryo
3	chr6:29425960-29426010	AG04450	lung:	fetal
4	chr6:29425960-29426010	NHBE	bronchial:	n/a
5	chr6:29425960-29426010	RPTEC	kidney:	n/a
6	chr6:29425960-29426010	HCF	heart:	n/a
7	chr6:29425960-29426010	Hela-S3	cervix:	n/a
8	chr6:29425960-29426010	U87	brain:	n/a
9	chr6:29425960-29426010	SK-N-MC	brain:	n/a
10	chr6:29425960-29426010	GM12878	blood:	n/a
11	chr6:29425960-29426010	NT2-D1	testis:	n/a
12	chr6:29425960-29426010	NB4	blood:	n/a
13	chr6:29425960-29426010	GM12892	blood:	n/a
14	chr6:29425960-29426010	PANC-1	pancreas:	n/a
15	chr6:29425960-29426010	HCT-116	colon:	n/a
16	chr6:29425960-29426010	T-47D	breast:	n/a
17	chr6:29425960-29426010	HUVEC	blood vessel:	n/a
18	chr6:29425960-29426010	HIPEpiC	eye:	n/a
19	chr6:29425960-29426010	BE2_C	brain:	n/a
20	chr6:29425960-29426010	SK-N-SH_RA	brain:	n/a
21	chr6:29425960-29426010	HL-60	blood:	n/a
22	chr6:29425960-29426010	HRE	kidney:	n/a
23	chr6:29425960-29426010	AG09319	gingival:	n/a
24	chr6:29425960-29426010	A549	lung:	n/a
25	chr6:29425960-29426010	LNCaP	prostate:	n/a
26	chr6:29425960-29426010	Caco-2	colon:	n/a
27	chr6:29425960-29426010	AG04449	skin:	fetal
28	chr6:29425960-29426010	ECC-1	luminal epithelium:	n/a
29	chr6:29425960-29426010	MCF10A-Er-Src	breast:	n/a
30	chr6:29425960-29426010	AoSMC	blood vessel:	n/a
31	chr6:29425960-29426010	AG09309	skin:	n/a
32	chr6:29425960-29426010	HEEpiC	esophagus:	n/a
33	chr6:29425960-29426010	HRPEpiC	eye:	n/a
34	chr6:29425960-29426010	HEK293	kidney:	embryo
35	chr6:29425960-29426010	Jurkat	blood:	n/a
36	chr6:29425960-29426010	MCF-7	breast:	n/a
37	chr6:29425960-29426010	PFSK-1	brain:	n/a
38	chr6:29425960-29426010	HRCEpiC	kidney:	n/a
39	chr6:29425960-29426010	K562	blood:	n/a
40	chr6:29425960-29426010	SAEC	small airway:	n/a
41	chr6:29425960-29426010	NH-A	brain:	n/a
42	chr6:29425960-29426010	GM06990	blood:	n/a
43	chr6:29425960-29426010	ovcar-3	ovarian:	n/a
44	chr6:29425960-29426010	HMEC	breast:	n/a
45	chr6:29425960-29426010	AG10803	skin:	n/a
46	chr6:29425960-29426010	ProgFib	skin:	n/a
47	chr6:29425960-29426010	HPAEpiC	pulmonary alveolar:	n/a
48	chr6:29425960-29426010	HepG2	liver:	n/a
49	chr6:29425960-29426010	GM12891	blood:	n/a
50	chr6:29425960-29426010	SK-N-SH	brain:	n/a

No data

Variant related genes	Relation type
OR2H1	CpG island
OR11A1	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1362075	0.81[EUR][1000 genomes]
rs1592412	0.81[EUR][1000 genomes]
rs2074464	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2107191	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094561	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3094564	0.80[EUR][1000 genomes]
rs3094572	0.81[EUR][1000 genomes]
rs3094573	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094574	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3128844	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3128854	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130852	0.81[EUR][1000 genomes]
rs3130854	0.80[EUR][1000 genomes]
rs3131019	0.81[EUR][1000 genomes]
rs734959	0.81[EUR][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	nsv830624	chr6:29274525-29445565	Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3117194	ZKSCAN3	cis	cerebellum	SCAN
rs3117194	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3117194	SLC17A3	cis	parietal	SCAN
rs3117194	ZNF192	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29418400-29427400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:29423800-29426200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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