Variant report

Variant	rs990416
Chromosome Location	chr2:173936921-173936922
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: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	chr2:173936880-173936930	HRPEpiC	eye:	n/a
2	chr2:173936880-173936930	PANC-1	pancreas:	n/a
3	chr2:173936880-173936930	MCF10A-Er-Src	breast:	n/a
4	chr2:173936880-173936930	ProgFib	skin:	n/a
5	chr2:173936880-173936930	SK-N-SH_RA	brain:	n/a
6	chr2:173936880-173936930	HUVEC	blood vessel:	n/a
7	chr2:173936880-173936930	RPTEC	kidney:	n/a
8	chr2:173936880-173936930	HL-60	blood:	n/a
9	chr2:173936880-173936930	HRE	kidney:	n/a
10	chr2:173936880-173936930	AG04450	lung:	fetal
11	chr2:173936880-173936930	Jurkat	blood:	n/a
12	chr2:173936880-173936930	ECC-1	luminal epithelium:	n/a
13	chr2:173936880-173936930	CMK	blood:	n/a
14	chr2:173936880-173936930	NT2-D1	testis:	n/a
15	chr2:173936880-173936930	HPAEpiC	pulmonary alveolar:	n/a
16	chr2:173936880-173936930	AG09309	skin:	n/a
17	chr2:173936880-173936930	AoSMC	blood vessel:	n/a
18	chr2:173936880-173936930	Hela-S3	cervix:	n/a
19	chr2:173936880-173936930	A549	lung:	n/a
20	chr2:173936880-173936930	Caco-2	colon:	n/a
21	chr2:173936880-173936930	HCPEpiC	choroid plexus:	n/a
22	chr2:173936880-173936930	PFSK-1	brain:	n/a
23	chr2:173936880-173936930	NH-A	brain:	n/a
24	chr2:173936880-173936930	BJ	skin:	n/a
25	chr2:173936880-173936930	PrEC	prostate:	n/a
26	chr2:173936880-173936930	NB4	blood:	n/a
27	chr2:173936880-173936930	MCF-7	breast:	n/a
28	chr2:173936880-173936930	AG10803	skin:	n/a
29	chr2:173936880-173936930	ovcar-3	ovarian:	n/a
30	chr2:173936880-173936930	GM06990	blood:	n/a
31	chr2:173936880-173936930	LNCaP	prostate:	n/a
32	chr2:173936880-173936930	U87	brain:	n/a
33	chr2:173936880-173936930	SKMC	muscle:	n/a
34	chr2:173936880-173936930	HIPEpiC	eye:	n/a
35	chr2:173936880-173936930	SAEC	small airway:	n/a
36	chr2:173936880-173936930	SK-N-MC	brain:	n/a
37	chr2:173936880-173936930	NHDF-neo	bronchial:	n/a
38	chr2:173936880-173936930	BE2_C	brain:	n/a
39	chr2:173936880-173936930	NHBE	bronchial:	n/a
40	chr2:173936880-173936930	GM12891	blood:	n/a
41	chr2:173936880-173936930	H1-hESC	embryonic stem cell:	embryo
42	chr2:173936880-173936930	HepG2	liver:	n/a
43	chr2:173936880-173936930	K562	blood:	n/a
44	chr2:173936880-173936930	HEEpiC	esophagus:	n/a
45	chr2:173936880-173936930	HCM	heart:	n/a
46	chr2:173936880-173936930	HCT-116	colon:	n/a
47	chr2:173936880-173936930	GM12892	blood:	n/a
48	chr2:173936880-173936930	AG09319	gingival:	n/a
49	chr2:173936880-173936930	HAEpiC	amniotic membrane:	n/a
50	chr2:173936880-173936930	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173931458..173934623-chr2:173936258..173938174,3	MCF-7	breast:
2	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091436	CpG island
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10180382	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11681384	1.00[ASN][1000 genomes]
rs11692252	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1545516	0.89[ASN][1000 genomes]
rs2034647	0.89[ASN][1000 genomes]
rs2044515	0.89[ASN][1000 genomes]
rs2358084	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754748	0.99[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769207	0.89[ASN][1000 genomes]
rs6718374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727541	0.82[ASN][1000 genomes]
rs6733082	0.86[ASN][1000 genomes]
rs6758859	0.81[ASN][1000 genomes]
rs7558132	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608532	0.95[ASN][1000 genomes]
rs9636294	0.86[ASN][1000 genomes]
rs989531	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989532	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs990417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs990416	ZAK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173920600-173937200	Weak transcription	Psoas Muscle	Psoas
2	chr2:173934000-173940000	Weak transcription	Pancreas	Pancrea
3	chr2:173935600-173939800	Weak transcription	Fetal Lung	lung
4	chr2:173936000-173937200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:173936000-173940000	Weak transcription	Right Atrium	heart

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