Variant report

Variant	rs34146962
Chromosome Location	chr3:48343307-48343308
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	POLR2A	chr3:48342391-48343691	MCF-7	breast:	n/a	n/a
5	BHLHE40	chr3:48342546-48343712	GM12878	blood:	n/a	chr3:48342640-48342656
6	POLR2A	chr3:48342366-48343522	GM12878	blood:	n/a	n/a
7	SRF	chr3:48342554-48343352	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:48342440-48343353	K562	blood:	n/a	n/a
9	MAX	chr3:48342505-48343682	H1-hESC	embryonic stem cell:	n/a	chr3:48342982-48342991
10	MAX	chr3:48341780-48343638	NB4	blood:	n/a	chr3:48342982-48342991
11	MAZ	chr3:48342622-48343556	Hela-S3	cervix:	n/a	chr3:48342982-48342991
12	CREB1	chr3:48342520-48343311	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr3:48342539-48343345	PANC-1	pancreas:	n/a	n/a
14	JUN	chr3:48342382-48343697	K562	blood:	n/a	n/a
15	POLR2A	chr3:48341465-48343731	K562	blood:	n/a	n/a
16	NFIC	chr3:48341637-48343830	GM12878	blood:	n/a	chr3:48343461-48343478 chr3:48343461-48343477
17	KAP1	chr3:48342543-48343419	HEK293	kidney:	n/a	chr3:48343249-48343257
18	MAX	chr3:48341832-48343643	K562	blood:	n/a	chr3:48342982-48342991
19	SIN3A	chr3:48342553-48343359	GM12878	blood:	n/a	chr3:48343153-48343162
20	POLR2A	chr3:48341101-48344338	GM12878	blood:	n/a	n/a
21	MAX	chr3:48342507-48343340	H1-hESC	embryonic stem cell:	n/a	chr3:48342982-48342991
22	GATA3	chr3:48342477-48343327	A549	lung:	n/a	n/a
23	CREB1	chr3:48342481-48343726	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:48342447-48343637	HepG2	liver:	n/a	n/a
25	ZEB1	chr3:48342539-48343664	GM12878	blood:	n/a	chr3:48343472-48343483
26	POLR2A	chr3:48342384-48343720	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:48342432-48343549	IMR90	lung:	n/a	n/a
28	POLR2A	chr3:48342442-48343430	Gliobla	brain:	n/a	n/a
29	EBF1	chr3:48342806-48343648	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:48342350-48343479	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:48342229-48343689	SK-N-MC	brain:	n/a	n/a
32	RELA	chr3:48342521-48343555	GM12892	blood:	n/a	chr3:48342999-48343008 chr3:48342999-48343008
33	E2F6	chr3:48342526-48343702	Hela-S3	cervix:	n/a	n/a
34	EP300	chr3:48342753-48343595	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:48342437-48343617	GM12878	blood:	n/a	n/a
36	UBTF	chr3:48342533-48343453	K562	blood:	n/a	n/a
37	SIN3AK20	chr3:48342526-48343814	MCF-7	breast:	n/a	n/a
38	ELF1	chr3:48342361-48343594	GM12878	blood:	n/a	n/a
39	MTA3	chr3:48342900-48343674	GM12878	blood:	n/a	n/a
40	CHD2	chr3:48342537-48343690	Hela-S3	cervix:	n/a	n/a
41	BRCA1	chr3:48342766-48343662	Hela-S3	cervix:	n/a	n/a
42	RELA	chr3:48342635-48343541	GM19193	blood:	n/a	chr3:48342999-48343008 chr3:48342999-48343008
43	GABPA	chr3:48342815-48343369	SK-N-SH	brain:	n/a	n/a
44	CREB1	chr3:48342756-48343323	ECC-1	luminal epithelium:	n/a	n/a
45	SMARCB1	chr3:48342389-48343665	Hela-S3	cervix:	n/a	n/a
46	MAX	chr3:48342368-48343696	SK-N-SH	brain:	n/a	chr3:48342982-48342991
47	MAX	chr3:48341811-48343777	HepG2	liver:	n/a	chr3:48342982-48342991
48	POLR2A	chr3:48342372-48343655	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr3:48341561-48343847	GM12892	blood:	n/a	n/a
50	POLR2A	chr3:48342370-48343494	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48343201..48345959-chr3:48358674..48361429,2	MCF-7	breast:
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	chr11:66383445..66384405-chr3:48343074..48343696,2	Hela-S3	cervix:
11	chr3:48341910..48343501-chr3:48486949..48488485,2	MCF-7	breast:
12	chr3:48341768..48344382-chr3:48487005..48489358,2	K562	blood:
13	chr3:48335073..48340448-chr3:48341483..48344077,7	K562	blood:
14	chr19:3557179..3557989-chr3:48343005..48343718,2	Hela-S3	cervix:
15	chr3:48342750..48344803-chr3:48480393..48482278,2	MCF-7	breast:

Variant related genes	Relation type
NME6	TF binding region
ENSG00000164051	Chromatin interaction
ENSG00000119725	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000161091	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000145779	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000113739	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000172113	Chromatin interaction
ENSG00000252466	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

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]
rs1459247	0.84[AFR][1000 genomes]
rs34136919	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34373799	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	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73831565	0.82[AFR][1000 genomes]
rs73831566	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642363	0.81[EUR][1000 genomes]
rs876597	0.82[AFR][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	chr3:48341800-48343800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr3:48341800-48343800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:48341800-48343800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:48341800-48343800	Flanking Active TSS	HMEC	breast
5	chr3:48342000-48343600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:48342000-48343600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:48342000-48343600	Active TSS	Ovary	ovary
8	chr3:48342000-48343800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:48342200-48343400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:48342200-48343400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:48342200-48343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:48342200-48343400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:48342200-48343400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:48342200-48343400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:48342200-48343400	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr3:48342200-48343400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:48342200-48343400	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr3:48342200-48343400	Active TSS	Aorta	Aorta
19	chr3:48342200-48343400	Active TSS	Brain Angular Gyrus	brain
20	chr3:48342200-48343400	Active TSS	Brain Anterior Caudate	brain
21	chr3:48342200-48343400	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:48342200-48343400	Active TSS	Brain Substantia Nigra	brain
23	chr3:48342200-48343400	Active TSS	Duodenum Mucosa	Duodenum
24	chr3:48342200-48343400	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr3:48342200-48343400	Active TSS	Fetal Heart	heart
26	chr3:48342200-48343400	Active TSS	Fetal Lung	lung
27	chr3:48342200-48343400	Active TSS	Fetal Stomach	stomach
28	chr3:48342200-48343400	Active TSS	Pancreas	Pancrea
29	chr3:48342200-48343400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:48342200-48343400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:48342200-48343400	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr3:48342200-48343400	Active TSS	Stomach Mucosa	stomach
33	chr3:48342200-48343400	Active TSS	Spleen	Spleen
34	chr3:48342200-48343400	Active TSS	Hela-S3	cervix
35	chr3:48342200-48343400	Active TSS	HepG2	liver
36	chr3:48342200-48343400	Active TSS	K562	blood
37	chr3:48342200-48343400	Active TSS	NHEK	skin
38	chr3:48342200-48343600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:48342200-48343600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:48342200-48343600	Active TSS	Esophagus	oesophagus
41	chr3:48342200-48343600	Active TSS	Fetal Kidney	kidney
42	chr3:48342200-48343600	Active TSS	Gastric	stomach
43	chr3:48342200-48343600	Active TSS	Lung	lung
44	chr3:48342200-48343600	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr3:48342200-48343800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr3:48342200-48343800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr3:48342200-48343800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:48342200-48343800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:48342200-48343800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:48342200-48343800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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