Variant report

Variant	rs34373799
Chromosome Location	chr3:48343006-48343007
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:471)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:471 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr3:48342472-48343340	GM12878	blood:	n/a	chr3:48342982-48342991
2	NRF1	chr3:48342672-48343494	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48341816-48344787	Raji	blood:	n/a	n/a
4	GABPA	chr3:48342830-48343244	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:48342391-48343691	MCF-7	breast:	n/a	n/a
6	GABPA	chr3:48342814-48343102	A549	lung:	n/a	n/a
7	BHLHE40	chr3:48342546-48343712	GM12878	blood:	n/a	chr3:48342640-48342656
8	POLR2A	chr3:48342366-48343522	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:48342545-48343231	A549	lung:	n/a	n/a
10	SRF	chr3:48342554-48343352	MCF-7	breast:	n/a	n/a
11	TAF1	chr3:48342351-48343286	H1-neurons	neurons:	n/a	n/a
12	ATF2	chr3:48342385-48343201	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:48342440-48343353	K562	blood:	n/a	n/a
14	MAX	chr3:48342505-48343682	H1-hESC	embryonic stem cell:	n/a	chr3:48342982-48342991
15	MAX	chr3:48341780-48343638	NB4	blood:	n/a	chr3:48342982-48342991
16	MAZ	chr3:48342622-48343556	Hela-S3	cervix:	n/a	chr3:48342982-48342991
17	CREB1	chr3:48342520-48343311	H1-hESC	embryonic stem cell:	n/a	n/a
18	SETDB1	chr3:48342727-48343230	K562	blood:	n/a	n/a
19	SIN3AK20	chr3:48342539-48343345	PANC-1	pancreas:	n/a	n/a
20	CTCF	chr3:48342860-48343010	HCPEpiC	choroid plexus:	n/a	n/a
21	MAX	chr3:48342699-48343180	H1-hESC	embryonic stem cell:	n/a	chr3:48342982-48342991
22	JUN	chr3:48342382-48343697	K562	blood:	n/a	n/a
23	POLR2A	chr3:48341465-48343731	K562	blood:	n/a	n/a
24	NFIC	chr3:48341637-48343830	GM12878	blood:	n/a	chr3:48343461-48343478 chr3:48343461-48343477
25	HEY1	chr3:48342481-48343300	HepG2	liver:	n/a	chr3:48342738-48342753
26	MYC	chr3:48342490-48343283	MCF-7	breast:	n/a	chr3:48342982-48342991
27	KAP1	chr3:48342543-48343419	HEK293	kidney:	n/a	chr3:48343249-48343257
28	MAX	chr3:48341832-48343643	K562	blood:	n/a	chr3:48342982-48342991
29	SIN3A	chr3:48342553-48343359	GM12878	blood:	n/a	chr3:48343153-48343162
30	POLR2A	chr3:48341101-48344338	GM12878	blood:	n/a	n/a
31	MAX	chr3:48342507-48343340	H1-hESC	embryonic stem cell:	n/a	chr3:48342982-48342991
32	GATA3	chr3:48342477-48343327	A549	lung:	n/a	n/a
33	CREB1	chr3:48342481-48343726	GM12878	blood:	n/a	n/a
34	BACH1	chr3:48342501-48343162	H1-hESC	embryonic stem cell:	n/a	n/a
35	ELK1	chr3:48342529-48343216	GM12878	blood:	n/a	n/a
36	HMGN3	chr3:48342521-48343279	K562	blood:	n/a	n/a
37	POLR2A	chr3:48342447-48343637	HepG2	liver:	n/a	n/a
38	ZEB1	chr3:48342539-48343664	GM12878	blood:	n/a	chr3:48343472-48343483
39	POLR2A	chr3:48342384-48343720	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:48342432-48343549	IMR90	lung:	n/a	n/a
41	POLR2A	chr3:48342442-48343430	Gliobla	brain:	n/a	n/a
42	EBF1	chr3:48342771-48343304	GM12878	blood:	n/a	n/a
43	EBF1	chr3:48342806-48343648	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:48342350-48343479	MCF-7	breast:	n/a	n/a
45	POLR2A	chr3:48342229-48343689	SK-N-MC	brain:	n/a	n/a
46	RELA	chr3:48342521-48343555	GM12892	blood:	n/a	chr3:48342999-48343008 chr3:48342999-48343008
47	MYC	chr3:48342737-48343062	H1-hESC	embryonic stem cell:	n/a	chr3:48342982-48342991
48	E2F6	chr3:48342526-48343702	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:48342619-48343241	SK-N-MC	brain:	n/a	n/a
50	ZBTB33	chr3:48342808-48343171	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48342999-48343049	MCF10A-Er-Src	breast:	n/a
2	chr3:48342999-48343049	HCPEpiC	choroid plexus:	n/a
3	chr3:48342999-48343049	Jurkat	blood:	n/a
4	chr3:48342999-48343049	AG09319	gingival:	n/a
5	chr3:48342999-48343049	HL-60	blood:	n/a
6	chr3:48342999-48343049	HRPEpiC	eye:	n/a
7	chr3:48342999-48343049	PFSK-1	brain:	n/a
8	chr3:48342999-48343049	ovcar-3	ovarian:	n/a
9	chr3:48342999-48343049	HIPEpiC	eye:	n/a
10	chr3:48342999-48343049	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:48342999-48343049	HUVEC	blood vessel:	n/a
12	chr3:48342999-48343049	RPTEC	kidney:	n/a
13	chr3:48342999-48343049	Hela-S3	cervix:	n/a
14	chr3:48342999-48343049	NHDF-neo	bronchial:	n/a
15	chr3:48342999-48343049	NT2-D1	testis:	n/a
16	chr3:48342999-48343049	BE2_C	brain:	n/a
17	chr3:48342999-48343049	ProgFib	skin:	n/a
18	chr3:48342999-48343049	K562	blood:	n/a
19	chr3:48342999-48343049	HepG2	liver:	n/a
20	chr3:48342999-48343049	HCF	heart:	n/a
21	chr3:48342999-48343049	Caco-2	colon:	n/a
22	chr3:48342999-48343049	AG04449	skin:	fetal
23	chr3:48342999-48343049	MCF-7	breast:	n/a
24	chr3:48342999-48343049	LNCaP	prostate:	n/a
25	chr3:48342999-48343049	AG04450	lung:	fetal
26	chr3:48342999-48343049	GM12892	blood:	n/a
27	chr3:48342999-48343049	GM06990	blood:	n/a
28	chr3:48342999-48343049	NHBE	bronchial:	n/a
29	chr3:48342999-48343049	SK-N-SH_RA	brain:	n/a
30	chr3:48342999-48343049	NH-A	brain:	n/a
31	chr3:48342999-48343049	HCM	heart:	n/a
32	chr3:48342999-48343049	GM12891	blood:	n/a
33	chr3:48342999-48343049	HMEC	breast:	n/a
34	chr3:48342999-48343049	SKMC	muscle:	n/a
35	chr3:48342999-48343049	Hepatocyte	liver:	n/a
36	chr3:48342999-48343049	GM12878	blood:	n/a
37	chr3:48342999-48343049	H1-hESC	embryonic stem cell:	embryo
38	chr3:48342999-48343049	NB4	blood:	n/a
39	chr3:48342999-48343049	SK-N-SH	brain:	n/a
40	chr3:48342999-48343049	PANC-1	pancreas:	n/a
41	chr3:48342999-48343049	HRE	kidney:	n/a
42	chr3:48342999-48343049	BJ	skin:	n/a
43	chr3:48342999-48343049	SK-N-MC	brain:	n/a
44	chr3:48342999-48343049	T-47D	breast:	n/a
45	chr3:48342999-48343049	A549	lung:	n/a
46	chr3:48342999-48343049	CMK	blood:	n/a
47	chr3:48342999-48343049	HEEpiC	esophagus:	n/a
48	chr3:48342999-48343049	PrEC	prostate:	n/a
49	chr3:48342999-48343049	GM19239	blood:	n/a
50	chr3:48342999-48343049	ECC-1	luminal epithelium:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:43010954..43011772-chr3:48342565..48343160,2	Hela-S3	cervix:
2	chr3:48342633..48343492-chr5:118604190..118604719,2	HCT-116	colon:
3	chr3:48341906..48343941-chr5:172755469..172757173,2	MCF-7	breast:
4	chr3:48341722..48343644-chr3:48355506..48358531,3	MCF-7	breast:
5	chr3:48342864..48345435-chr3:48356461..48358274,2	K562	blood:
6	chr3:48281295..48284269-chr3:48341390..48344515,3	MCF-7	breast:
7	chr14:74352828..74353780-chr3:48342768..48343476,2	HCT-116	colon:
8	chr3:48341336..48343730-chr3:48444609..48447589,3	K562	blood:
9	chr3:48341872..48344261-chr3:48469680..48472661,4	MCF-7	breast:
10	chr3:48341910..48343501-chr3:48486949..48488485,2	MCF-7	breast:
11	chr3:48341768..48344382-chr3:48487005..48489358,2	K562	blood:
12	chr3:48335073..48340448-chr3:48341483..48344077,7	K562	blood:
13	chr19:3557179..3557989-chr3:48343005..48343718,2	Hela-S3	cervix:
14	chr3:48342750..48344803-chr3:48480393..48482278,2	MCF-7	breast:

No data

Variant related genes	Relation type
NME6	TF binding region
NME6	CpG island
ENSG00000270022	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000161091	Chromatin interaction
ENSG00000113739	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000119725	Chromatin interaction
ENSG00000172113	Chromatin interaction
ENSG00000145779	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000252466	Chromatin interaction
ENSG00000164051	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11130161	0.81[EUR][1000 genomes]
rs11924352	0.81[EUR][1000 genomes]
rs12633518	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34136919	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34146962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57994790	0.86[EUR][1000 genomes]
rs58582477	0.82[EUR][1000 genomes]
rs60305502	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71323398	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73831561	0.81[EUR][1000 genomes]
rs73831563	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73831566	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642363	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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48341800-48343200	Active TSS	GM12878-XiMat	blood
2	chr3:48341800-48343800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:48341800-48343800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:48341800-48343800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:48341800-48343800	Flanking Active TSS	HMEC	breast
6	chr3:48342000-48343200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr3:48342000-48343600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr3:48342000-48343600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:48342000-48343600	Active TSS	Ovary	ovary
10	chr3:48342000-48343800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:48342200-48343200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:48342200-48343200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:48342200-48343200	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:48342200-48343200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:48342200-48343200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:48342200-48343200	Active TSS	Liver	Liver
17	chr3:48342200-48343200	Active TSS	Fetal Brain Female	brain
18	chr3:48342200-48343200	Active TSS	Stomach Smooth Muscle	stomach
19	chr3:48342200-48343200	Active TSS	HUVEC	blood vessel
20	chr3:48342200-48343200	Active TSS	Monocytes-CD14+_RO01746	blood
21	chr3:48342200-48343200	Active TSS	NH-A	brain
22	chr3:48342200-48343200	Active TSS	Osteobl	bone
23	chr3:48342200-48343400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:48342200-48343400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:48342200-48343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:48342200-48343400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:48342200-48343400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:48342200-48343400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:48342200-48343400	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:48342200-48343400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:48342200-48343400	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr3:48342200-48343400	Active TSS	Aorta	Aorta
33	chr3:48342200-48343400	Active TSS	Brain Angular Gyrus	brain
34	chr3:48342200-48343400	Active TSS	Brain Anterior Caudate	brain
35	chr3:48342200-48343400	Active TSS	Brain Cingulate Gyrus	brain
36	chr3:48342200-48343400	Active TSS	Brain Substantia Nigra	brain
37	chr3:48342200-48343400	Active TSS	Duodenum Mucosa	Duodenum
38	chr3:48342200-48343400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:48342200-48343400	Active TSS	Fetal Heart	heart
40	chr3:48342200-48343400	Active TSS	Fetal Lung	lung
41	chr3:48342200-48343400	Active TSS	Fetal Stomach	stomach
42	chr3:48342200-48343400	Active TSS	Pancreas	Pancrea
43	chr3:48342200-48343400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:48342200-48343400	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:48342200-48343400	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr3:48342200-48343400	Active TSS	Stomach Mucosa	stomach
47	chr3:48342200-48343400	Active TSS	Spleen	Spleen
48	chr3:48342200-48343400	Active TSS	Hela-S3	cervix
49	chr3:48342200-48343400	Active TSS	HepG2	liver
50	chr3:48342200-48343400	Active TSS	K562	blood

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