Variant report

Variant	rs34702539
Chromosome Location	chr2:178976821-178976822
allele	C/T
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	POLR2A	chr2:178976719-178977714	PFSK-1	brain:	n/a	n/a
2	HCFC1	chr2:178976699-178977667	Hela-S3	cervix:	n/a	n/a
3	ELF1	chr2:178976652-178977683	MCF-7	breast:	n/a	chr2:178977166-178977175 chr2:178977162-178977175 chr2:178977165-178977174
4	NR3C1	chr2:178976810-178977295	A549	lung:	n/a	n/a
5	GATA3	chr2:178976724-178977437	MCF-7	breast:	n/a	n/a
6	CEBPB	chr2:178976791-178977201	K562	blood:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
7	CBX3	chr2:178976748-178977833	HCT-116	colon:	n/a	n/a
8	CEBPB	chr2:178976775-178977353	Hela-S3	cervix:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
9	HA-E2F1	chr2:178976802-178977502	MCF-7	breast:	n/a	chr2:178977143-178977153
10	CTCF	chr2:178976813-178977352	A549	lung:	n/a	chr2:178977085-178977095 chr2:178977083-178977096 chr2:178977081-178977097 chr2:178977080-178977098
11	CBX3	chr2:178976684-178977547	HCT-116	colon:	n/a	n/a
12	CEBPB	chr2:178976753-178977242	ECC-1	luminal epithelium:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
13	TEAD4	chr2:178976732-178977322	HepG2	liver:	n/a	n/a
14	CTCF	chr2:178976784-178977785	HCT-116	colon:	n/a	chr2:178977085-178977095 chr2:178977083-178977096 chr2:178977081-178977097 chr2:178977080-178977098
15	NFIC	chr2:178976802-178977467	HepG2	liver:	n/a	n/a
16	CEBPB	chr2:178976675-178977379	K562	blood:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
17	GATA2	chr2:178976820-178977391	HUVEC	blood vessel:	n/a	n/a
18	GATA3	chr2:178976685-178977333	SH-SY5Y	brain:	n/a	n/a
19	MXI1	chr2:178976593-178978663	SK-N-SH	brain:	n/a	n/a
20	REST	chr2:178976794-178977725	HepG2	liver:	n/a	chr2:178977695-178977705 chr2:178976979-178976986 chr2:178977639-178977652 chr2:178977135-178977144 chr2:178977103-178977113
21	MAZ	chr2:178976720-178978152	IMR90	lung:	n/a	n/a
22	CTCF	chr2:178976709-178977417	MCF-7	breast:	n/a	chr2:178977085-178977095 chr2:178977083-178977096 chr2:178977081-178977097 chr2:178977080-178977098
23	CEBPB	chr2:178976600-178977396	A549	lung:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
24	BCL3	chr2:178976764-178977570	A549	lung:	n/a	chr2:178977137-178977145
25	GABPA	chr2:178976759-178977489	SK-N-SH	brain:	n/a	n/a
26	GATA2	chr2:178976785-178977451	K562	blood:	n/a	n/a
27	GATA2	chr2:178976656-178977628	SH-SY5Y	brain:	n/a	n/a
28	REST	chr2:178976711-178978040	H1-neurons	neurons:	n/a	chr2:178977695-178977705 chr2:178976979-178976986 chr2:178977639-178977652 chr2:178977135-178977144 chr2:178977103-178977113
29	GATA3	chr2:178976645-178977579	A549	lung:	n/a	n/a
30	GATA3	chr2:178976777-178977383	T-47D	breast:	n/a	n/a
31	PML	chr2:178976813-178977528	MCF-7	breast:	n/a	n/a
32	EP300	chr2:178976730-178977567	SK-N-SH	brain:	n/a	n/a
33	CEBPB	chr2:178976727-178977277	A549	lung:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
34	CEBPB	chr2:178976811-178977243	K562	blood:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
35	CTCF	chr2:178976753-178976832	GM10266	blood:	n/a	n/a
36	NFIC	chr2:178976783-178977602	HepG2	liver:	n/a	n/a
37	MAZ	chr2:178976770-178977335	HepG2	liver:	n/a	n/a
38	HDAC2	chr2:178976803-178977698	MCF-7	breast:	n/a	n/a
39	GABPA	chr2:178976812-178977428	A549	lung:	n/a	n/a
40	GATA2	chr2:178976800-178977310	K562	blood:	n/a	n/a
41	TFAP2C	chr2:178976659-178977802	Hela-S3	cervix:	n/a	chr2:178976986-178977001 chr2:178977594-178977609
42	EP300	chr2:178976809-178977420	A549	lung:	n/a	n/a
43	KAP1	chr2:178976648-178977676	HEK293	kidney:	n/a	n/a
44	ETS1	chr2:178976766-178977574	A549	lung:	n/a	chr2:178977166-178977177 chr2:178977091-178977104 chr2:178977167-178977177
45	RAD21	chr2:178976811-178977326	A549	lung:	n/a	chr2:178977081-178977100 chr2:178977086-178977098 chr2:178977086-178977096
46	TCF12	chr2:178976787-178977812	ECC-1	luminal epithelium:	n/a	chr2:178977636-178977646
47	CEBPB	chr2:178976793-178977216	IMR90	lung:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
48	GABPA	chr2:178976636-178977813	MCF-7	breast:	n/a	n/a
49	CEBPB	chr2:178976807-178977202	A549	lung:	n/a	chr2:178977004-178977013 chr2:178977002-178977015 chr2:178977002-178977013
50	BCL3	chr2:178976708-178977347	A549	lung:	n/a	chr2:178977137-178977145

No.	Distal block	Cell Line	Cell type
1	chr2:178970656..178974678-chr2:178975520..178979270,3	K562	blood:
2	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
3	chr2:178975231..178977429-chr2:179315218..179317152,2	MCF-7	breast:
4	chr2:178976808..178978488-chr2:179342162..179344754,2	MCF-7	breast:
5	chr2:178975761..178978600-chr2:179056476..179059620,3	K562	blood:
6	chr2:178975067..178978289-chr2:179058254..179060575,4	MCF-7	breast:
7	chr2:178974707..178979925-chr2:179277151..179280371,6	K562	blood:
8	chr2:178972756..178975132-chr2:178975866..178978416,2	MCF-7	breast:
9	chr2:178976079..178979038-chr2:178986555..178992721,6	MCF-7	breast:
10	chr2:178976419..178978821-chr2:179313368..179316809,4	K562	blood:

Variant related genes	Relation type
PDE11A	TF binding region
RBM45	TF binding region
ENSG00000079150	Chromatin interaction
ENSG00000128655	Chromatin interaction
ENSG00000079156	Chromatin interaction
ENSG00000155636	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000223960	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12989423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989778	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033194	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419755	1.00[ASN][1000 genomes]
rs334055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334065	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334073	0.94[AFR][1000 genomes]
rs334076	1.00[ASN][1000 genomes]
rs334077	1.00[ASN][1000 genomes]
rs34069002	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34395717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34927879	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35620189	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35938761	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423555	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv518790	chr2:178963445-179000291	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178973200-178977000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:178976400-178977000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
3	chr2:178976600-178977000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:178976600-178977000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:178976600-178977000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr2:178976600-178977000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr2:178976600-178977000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr2:178976600-178977000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:178976600-178977000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:178976600-178977000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:178976600-178977000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:178976600-178977000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr2:178976600-178977000	Enhancers	Right Ventricle	heart
14	chr2:178976600-178977000	Enhancers	Spleen	Spleen
15	chr2:178976600-178977000	Flanking Active TSS	Dnd41	blood
16	chr2:178976600-178977000	Enhancers	NHDF-Ad	bronchial
17	chr2:178976600-178977000	Flanking Active TSS	NHEK	skin
18	chr2:178976600-178977000	Enhancers	NHLF	lung
19	chr2:178976600-178977200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:178976600-178977800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr2:178976600-178978000	Active TSS	Lung	lung
22	chr2:178976800-178977000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:178976800-178977000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:178976800-178977000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:178976800-178977000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:178976800-178977000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:178976800-178977000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:178976800-178977000	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr2:178976800-178977000	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr2:178976800-178977000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:178976800-178977000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:178976800-178977000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:178976800-178977000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:178976800-178977000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:178976800-178977000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:178976800-178977000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:178976800-178977000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:178976800-178977000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:178976800-178977000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:178976800-178977000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:178976800-178977000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:178976800-178977000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr2:178976800-178977000	Enhancers	Liver	Liver
44	chr2:178976800-178977000	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr2:178976800-178977000	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr2:178976800-178977000	Enhancers	Esophagus	oesophagus
47	chr2:178976800-178977000	Enhancers	Fetal Muscle Leg	muscle
48	chr2:178976800-178977000	Flanking Active TSS	Placenta	Placenta
49	chr2:178976800-178977000	Enhancers	Fetal Stomach	stomach
50	chr2:178976800-178977000	Enhancers	Left Ventricle	heart

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