Variant report

Variant	rs339723
Chromosome Location	chr3:42700630-42700631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr3:42700432-42701333	K562	blood:	n/a	chr3:42700704-42700725
2	SPI1	chr3:42700491-42700925	HL-60	blood:	n/a	n/a
3	ZNF263	chr3:42700448-42702000	HEK293-T-REx	kidney:	n/a	chr3:42700704-42700725 chr3:42701783-42701792
4	POLR2A	chr3:42700568-42700768	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42700585-42700635	PrEC	prostate:	n/a
2	chr3:42700585-42700635	HCT-116	colon:	n/a
3	chr3:42700585-42700635	HL-60	blood:	n/a
4	chr3:42700585-42700635	Caco-2	colon:	n/a
5	chr3:42700585-42700635	ECC-1	luminal epithelium:	n/a
6	chr3:42700585-42700635	ovcar-3	ovarian:	n/a
7	chr3:42700585-42700635	GM12878	blood:	n/a
8	chr3:42700585-42700635	HEEpiC	esophagus:	n/a
9	chr3:42700585-42700635	AG04449	skin:	fetal
10	chr3:42700585-42700635	AG09319	gingival:	n/a
11	chr3:42700585-42700635	HRPEpiC	eye:	n/a
12	chr3:42700585-42700635	SK-N-SH_RA	brain:	n/a
13	chr3:42700585-42700635	HPAEpiC	pulmonary alveolar:	n/a
14	chr3:42700585-42700635	NHDF-neo	bronchial:	n/a
15	chr3:42700585-42700635	GM19239	blood:	n/a
16	chr3:42700585-42700635	AG09309	skin:	n/a
17	chr3:42700585-42700635	HRCEpiC	kidney:	n/a
18	chr3:42700585-42700635	H1-hESC	embryonic stem cell:	embryo
19	chr3:42700585-42700635	AoSMC	blood vessel:	n/a
20	chr3:42700585-42700635	K562	blood:	n/a
21	chr3:42700585-42700635	T-47D	breast:	n/a
22	chr3:42700585-42700635	ProgFib	skin:	n/a
23	chr3:42700585-42700635	U87	brain:	n/a
24	chr3:42700585-42700635	AG10803	skin:	n/a
25	chr3:42700585-42700635	BE2_C	brain:	n/a
26	chr3:42700585-42700635	MCF10A-Er-Src	breast:	n/a
27	chr3:42700585-42700635	AG04450	lung:	fetal
28	chr3:42700585-42700635	IMR90	lung:	fetal
29	chr3:42700585-42700635	SKMC	muscle:	n/a
30	chr3:42700585-42700635	GM12892	blood:	n/a
31	chr3:42700585-42700635	GM06990	blood:	n/a
32	chr3:42700585-42700635	NT2-D1	testis:	n/a
33	chr3:42700585-42700635	NH-A	brain:	n/a
34	chr3:42700585-42700635	Hepatocyte	liver:	n/a
35	chr3:42700585-42700635	RPTEC	kidney:	n/a
36	chr3:42700585-42700635	Jurkat	blood:	n/a
37	chr3:42700585-42700635	PANC-1	pancreas:	n/a
38	chr3:42700585-42700635	HUVEC	blood vessel:	n/a
39	chr3:42700585-42700635	LNCaP	prostate:	n/a
40	chr3:42700585-42700635	HCM	heart:	n/a
41	chr3:42700585-42700635	SK-N-SH	brain:	n/a
42	chr3:42700585-42700635	SAEC	small airway:	n/a
43	chr3:42700585-42700635	HAEpiC	amniotic membrane:	n/a
44	chr3:42700585-42700635	BJ	skin:	n/a
45	chr3:42700585-42700635	HCF	heart:	n/a
46	chr3:42700585-42700635	PFSK-1	brain:	n/a
47	chr3:42700585-42700635	HRE	kidney:	n/a
48	chr3:42700585-42700635	NHBE	bronchial:	n/a
49	chr3:42700585-42700635	HepG2	liver:	n/a
50	chr3:42700585-42700635	NB4	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:42693324..42695216-chr3:42700072..42702167,2	MCF-7	breast:
2	chr3:42700054..42702957-chr3:42774515..42776215,2	K562	blood:
3	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:
4	chr3:42695218..42698513-chr3:42700428..42704457,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230084	TF binding region
ENSG00000230084	CpG island
ENSG00000230084	Chromatin interaction
ENSG00000244607	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2976533	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339658	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339725	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs339726	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs339727	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339728	0.87[AMR][1000 genomes]
rs339733	0.86[AMR][1000 genomes]
rs4549	0.82[AMR][1000 genomes]
rs586082	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs587712	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs597498	0.82[AMR][1000 genomes]
rs607568	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs612733	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs614323	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs617722	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs627664	0.82[AMR][1000 genomes]
rs638836	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs639692	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs640689	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs663673	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs689251	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs704979	0.80[AMR][1000 genomes]
rs8351	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs339723	NKTR	cis	Nerve Tibial	GTEx
rs339723	NKTR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42696800-42701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:42697000-42702400	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr3:42697200-42701400	Genic enhancers	Fetal Muscle Leg	muscle
4	chr3:42697200-42703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
6	chr3:42697400-42700800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:42697400-42701200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:42697400-42702000	Weak transcription	Fetal Kidney	kidney
9	chr3:42697400-42703000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:42697400-42706800	Weak transcription	HMEC	breast
11	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
13	chr3:42697600-42703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:42697600-42704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:42697600-42704800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:42697600-42707000	Weak transcription	A549	lung
17	chr3:42697600-42708000	Weak transcription	Colonic Mucosa	Colon
18	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:42697800-42701000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:42697800-42702200	Weak transcription	HSMMtube	muscle
21	chr3:42697800-42702600	Genic enhancers	Brain Hippocampus Middle	brain
22	chr3:42697800-42707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:42697800-42707600	Strong transcription	Fetal Intestine Small	intestine
24	chr3:42697800-42707800	Weak transcription	Psoas Muscle	Psoas
25	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:42698000-42701200	Weak transcription	NH-A	brain
27	chr3:42698000-42706400	Strong transcription	Fetal Stomach	stomach
28	chr3:42698200-42701200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:42698200-42701200	Weak transcription	Osteobl	bone
30	chr3:42698200-42706600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:42698200-42708000	Weak transcription	HSMM	muscle
32	chr3:42698200-42708400	Weak transcription	HUVEC	blood vessel
33	chr3:42698400-42701200	Strong transcription	NHLF	lung
34	chr3:42698400-42703800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:42698400-42704000	Genic enhancers	Right Ventricle	heart
36	chr3:42698600-42701200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:42698600-42701200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:42698600-42701400	Weak transcription	NHDF-Ad	bronchial
39	chr3:42698600-42703200	Genic enhancers	Stomach Smooth Muscle	stomach
40	chr3:42698800-42703400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:42699000-42701600	Strong transcription	Fetal Brain Female	brain
42	chr3:42699200-42702400	Strong transcription	Fetal Intestine Large	intestine
43	chr3:42699200-42702600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:42699400-42701000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:42699400-42701200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr3:42699400-42701200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:42699400-42701600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:42699400-42702000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:42699400-42703200	Enhancers	Fetal Heart	heart
50	chr3:42699400-42703400	Strong transcription	NHEK	skin

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