Variant report

Variant	rs664958
Chromosome Location	chr17:18287838-18287839
allele	A/C
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	chr17:18287814-18287864	AG09319	gingival:	n/a
2	chr17:18287814-18287864	GM12892	blood:	n/a
3	chr17:18287814-18287864	HEEpiC	esophagus:	n/a
4	chr17:18287814-18287864	SAEC	small airway:	n/a
5	chr17:18287814-18287864	SK-N-SH	brain:	n/a
6	chr17:18287814-18287864	GM12891	blood:	n/a
7	chr17:18287814-18287864	GM12878	blood:	n/a
8	chr17:18287814-18287864	GM06990	blood:	n/a
9	chr17:18287814-18287864	SK-N-SH_RA	brain:	n/a
10	chr17:18287814-18287864	ECC-1	luminal epithelium:	n/a
11	chr17:18287814-18287864	BE2_C	brain:	n/a
12	chr17:18287814-18287864	AG04449	skin:	fetal
13	chr17:18287814-18287864	HRPEpiC	eye:	n/a
14	chr17:18287814-18287864	PFSK-1	brain:	n/a
15	chr17:18287814-18287864	SK-N-MC	brain:	n/a
16	chr17:18287814-18287864	HRCEpiC	kidney:	n/a
17	chr17:18287814-18287864	HMEC	breast:	n/a
18	chr17:18287814-18287864	HAEpiC	amniotic membrane:	n/a
19	chr17:18287814-18287864	HCPEpiC	choroid plexus:	n/a
20	chr17:18287814-18287864	AG10803	skin:	n/a
21	chr17:18287814-18287864	K562	blood:	n/a
22	chr17:18287814-18287864	H1-hESC	embryonic stem cell:	embryo
23	chr17:18287814-18287864	T-47D	breast:	n/a
24	chr17:18287814-18287864	CMK	blood:	n/a
25	chr17:18287814-18287864	HCM	heart:	n/a
26	chr17:18287814-18287864	HPAEpiC	pulmonary alveolar:	n/a
27	chr17:18287814-18287864	GM19239	blood:	n/a
28	chr17:18287814-18287864	SKMC	muscle:	n/a
29	chr17:18287814-18287864	AG04450	lung:	fetal
30	chr17:18287814-18287864	HCT-116	colon:	n/a
31	chr17:18287814-18287864	Hela-S3	cervix:	n/a
32	chr17:18287814-18287864	U87	brain:	n/a
33	chr17:18287814-18287864	NT2-D1	testis:	n/a
34	chr17:18287814-18287864	NHDF-neo	bronchial:	n/a
35	chr17:18287814-18287864	HL-60	blood:	n/a
36	chr17:18287814-18287864	NH-A	brain:	n/a
37	chr17:18287814-18287864	Caco-2	colon:	n/a
38	chr17:18287814-18287864	A549	lung:	n/a
39	chr17:18287814-18287864	LNCaP	prostate:	n/a
40	chr17:18287814-18287864	ProgFib	skin:	n/a
41	chr17:18287814-18287864	HEK293	kidney:	embryo
42	chr17:18287814-18287864	HRE	kidney:	n/a
43	chr17:18287814-18287864	Hepatocyte	liver:	n/a
44	chr17:18287814-18287864	IMR90	lung:	fetal
45	chr17:18287814-18287864	HCF	heart:	n/a
46	chr17:18287814-18287864	AG09309	skin:	n/a
47	chr17:18287814-18287864	PANC-1	pancreas:	n/a
48	chr17:18287814-18287864	RPTEC	kidney:	n/a
49	chr17:18287814-18287864	HUVEC	blood vessel:	n/a
50	chr17:18287814-18287864	HepG2	liver:	n/a

No data

Variant related genes	Relation type
EVPLL	CpG island
ENSG00000267441	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1682280	0.87[ASN][1000 genomes]
rs2461847	0.83[ASN][1000 genomes]
rs34769815	0.83[ASN][1000 genomes]
rs573550	0.91[ASN][1000 genomes]
rs583792	0.92[ASN][1000 genomes]
rs584300	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs586757	0.82[ASN][1000 genomes]
rs664957	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7222009	0.81[ASN][1000 genomes]
rs7222335	0.84[ASN][1000 genomes]
rs779144	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
12	nsv827913	chr17:18253785-18572122	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1065708	chr17:18259174-18913343	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
14	nsv978378	chr17:18272529-18321736	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv962275	chr17:18272529-18471923	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv833388	chr17:18275146-18454773	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
17	nsv907778	chr17:18275847-18409309	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv469661	chr17:18275972-18446377	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
19	nsv482696	chr17:18275972-18446377	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
20	nsv827914	chr17:18278173-18424843	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1058895	chr17:18278477-18474634	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
22	esv3423559	chr17:18282155-18287887	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1062985	chr17:18283527-18465209	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
24	nsv1067238	chr17:18283687-18465209	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
25	nsv1057226	chr17:18283687-18510146	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
26	esv3373438	chr17:18285177-18295675	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	esv3341543	chr17:18285652-18288200	Bivalent Enhancer Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs664958	FAM106A	cis	lung	GTEx
rs664958	USP32P2	cis	Muscle Skeletal	GTEx
rs664958	SHMT1	cis	Whole Blood	GTEx
rs664958	USP32P2	cis	Thyroid	GTEx
rs664958	FAM106A	cis	Thyroid	GTEx
rs664958	USP32P2	cis	lung	GTEx
rs664958	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs664958	SHMT1	cis	Esophagus Muscularis	GTEx
rs664958	FAM106A	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18267200-18288200	Weak transcription	Right Atrium	heart
2	chr17:18283000-18288200	Enhancers	Fetal Thymus	thymus
3	chr17:18283800-18289400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr17:18287800-18290000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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