Variant report

Variant	rs554040452
Chromosome Location	chr2:172016354-172016355
allele	A/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	TAF1	chr2:172015986-172016620	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr2:172016177-172016519	HCT-116	colon:	n/a	n/a
3	BHLHE40	chr2:172016037-172016481	GM12878	blood:	n/a	n/a
4	RCOR1	chr2:172016310-172016512	K562	blood:	n/a	n/a
5	RFX5	chr2:172016027-172016463	HepG2	liver:	n/a	n/a
6	TCF12	chr2:172015626-172017580	A549	lung:	n/a	chr2:172017439-172017448
7	PML	chr2:172015589-172016620	K562	blood:	n/a	n/a
8	RUNX3	chr2:172015624-172016580	GM12878	blood:	n/a	chr2:172016053-172016070
9	GTF2F1	chr2:172016150-172016491	K562	blood:	n/a	n/a
10	POLR2A	chr2:172016027-172017981	NB4	blood:	n/a	n/a
11	CTCF	chr2:172016280-172016430	HRE	kidney:	n/a	n/a
12	POLR2A	chr2:172015653-172016690	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:172015773-172018047	GM18526	blood:	n/a	n/a
14	HDAC2	chr2:172015696-172016469	HepG2	liver:	n/a	n/a
15	YY1	chr2:172016156-172016680	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr2:172015911-172017997	GM12878	blood:	n/a	n/a
17	YY1	chr2:172015882-172018018	GM12892	blood:	n/a	chr2:172017415-172017426 chr2:172017541-172017552 chr2:172017417-172017426 chr2:172016885-172016905 chr2:172017414-172017423
18	NFATC1	chr2:172015709-172016408	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:172015367-172018060	GM12878	blood:	n/a	n/a
20	RELA	chr2:172015541-172016587	GM18951	blood:	n/a	n/a
21	MTA3	chr2:172015310-172017405	GM12878	blood:	n/a	n/a
22	STAT5A	chr2:172015572-172016564	GM12878	blood:	n/a	chr2:172016368-172016380
23	POLR2A	chr2:172016139-172017818	HEK293	kidney:	n/a	n/a
24	POLR2A	chr2:172015880-172016702	GM12892	blood:	n/a	n/a
25	MAX	chr2:172015708-172016733	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr2:172016222-172016587	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:172015995-172017988	GM12878	blood:	n/a	n/a
28	RCOR1	chr2:172015406-172016381	K562	blood:	n/a	n/a
29	POLR2A	chr2:172016316-172017842	A549	lung:	n/a	n/a
30	POLR2A	chr2:172015914-172016586	SK-N-MC	brain:	n/a	n/a
31	CEBPD	chr2:172015903-172016742	HepG2	liver:	n/a	n/a
32	BHLHE40	chr2:172015795-172016591	K562	blood:	n/a	n/a
33	TAF1	chr2:172016189-172016657	SK-N-SH	brain:	n/a	n/a
34	FOXM1	chr2:172015744-172016509	GM12878	blood:	n/a	n/a
35	POU2F2	chr2:172015756-172016597	GM12878	blood:	n/a	chr2:172016556-172016568
36	CTCF	chr2:172016300-172016450	SK-N-SH_RA	brain:	n/a	n/a
37	SMC3	chr2:172015703-172016473	HepG2	liver:	n/a	chr2:172015958-172015965 chr2:172015951-172015965
38	TBP	chr2:172015372-172018559	K562	blood:	n/a	n/a
39	POLR2A	chr2:172015923-172016676	GM12891	blood:	n/a	n/a
40	MAX	chr2:172015338-172017984	Hela-S3	cervix:	n/a	n/a
41	ELF1	chr2:172015896-172016706	GM12878	blood:	n/a	n/a
42	MXI1	chr2:172015314-172018623	IMR90	lung:	n/a	chr2:172017743-172017752
43	POU2F2	chr2:172016016-172016573	GM12891	blood:	n/a	chr2:172016556-172016568
44	POLR2A	chr2:172016235-172017969	A549	lung:	n/a	n/a
45	CTCF	chr2:172015492-172016720	SK-N-SH	brain:	n/a	chr2:172015949-172015967 chr2:172015944-172015965 chr2:172015950-172015966
46	POLR2A	chr2:172015946-172016688	K562	blood:	n/a	n/a
47	POLR2A	chr2:172015899-172018008	K562	blood:	n/a	n/a
48	SIN3A	chr2:172015299-172017992	H1-hESC	embryonic stem cell:	n/a	chr2:172017541-172017552
49	CHD2	chr2:172015679-172016662	GM12878	blood:	n/a	chr2:172016549-172016559
50	HNF4A	chr2:172015860-172016494	HepG2	liver:	n/a	chr2:172016235-172016250 chr2:172016429-172016444

No.	Distal block	Cell Line	Cell type
1	chr2:172013226..172020125-chr2:172287594..172292844,18	MCF-7	breast:
2	chr2:171921242..171923665-chr2:172015920..172017690,2	MCF-7	breast:
3	chr2:172016272..172018929-chr2:172086731..172089635,2	MCF-7	breast:
4	chr2:172015340..172019166-chr2:172288878..172291883,5	K562	blood:
5	chr2:171785349..171787069-chr2:172015224..172018585,4	MCF-7	breast:
6	chr2:172016279..172018303-chr2:172948918..172950727,3	MCF-7	breast:
7	chr1:149819814..149821730-chr2:172014247..172017009,2	K562	blood:
8	chr2:172014091..172018646-chr2:172288530..172293107,15	MCF-7	breast:
9	chr2:172013756..172019540-chr2:172285624..172293532,16	K562	blood:
10	chr2:171784510..171786977-chr2:172014779..172017241,3	K562	blood:
11	chr2:171810266..171813832-chr2:172014832..172018055,4	K562	blood:
12	chr2:172002500..172008778-chr2:172012564..172018500,9	MCF-7	breast:

Variant related genes	Relation type
TLK1	TF binding region
ENSG00000198586	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000115806	Chromatin interaction
ENSG00000261716	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000238567	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3420180	chr2:172015931-172018479	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	esv3355452	chr2:172016331-172018879	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 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	chr2:172013800-172018200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:172013800-172018200	Active TSS	GM12878-XiMat	blood
3	chr2:172014000-172018200	Active TSS	K562	blood
4	chr2:172014000-172018800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:172014200-172018600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:172014400-172018200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:172014400-172018200	Active TSS	HSMMtube	muscle
8	chr2:172014600-172016400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:172014600-172018400	Active TSS	Stomach Smooth Muscle	stomach
10	chr2:172014600-172018600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:172014600-172018600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:172014600-172018600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:172014600-172018600	Active TSS	HMEC	breast
14	chr2:172014800-172016400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr2:172014800-172016400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:172014800-172018000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:172014800-172018200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:172014800-172018400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr2:172014800-172018400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr2:172014800-172018400	Active TSS	HSMM	muscle
21	chr2:172015000-172016400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr2:172015000-172018000	Active TSS	Brain Anterior Caudate	brain
23	chr2:172015000-172018000	Active TSS	Osteobl	bone
24	chr2:172015000-172018200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:172015000-172018200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:172015000-172018200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:172015000-172018200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:172015000-172018200	Active TSS	Fetal Kidney	kidney
29	chr2:172015000-172018200	Active TSS	Hela-S3	cervix
30	chr2:172015000-172018400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:172015000-172018400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:172015000-172018400	Active TSS	Brain Cingulate Gyrus	brain
33	chr2:172015000-172018400	Active TSS	Colon Smooth Muscle	Colon
34	chr2:172015000-172018400	Active TSS	Fetal Brain Male	brain
35	chr2:172015000-172018400	Active TSS	NHLF	lung
36	chr2:172015200-172016400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr2:172015200-172017800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:172015200-172018000	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:172015200-172018000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:172015200-172018200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr2:172015200-172018200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr2:172015200-172018200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:172015200-172018200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:172015200-172018200	Active TSS	Placenta	Placenta
45	chr2:172015200-172018200	Active TSS	Fetal Stomach	stomach
46	chr2:172015200-172018200	Active TSS	A549	lung
47	chr2:172015200-172018400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:172015200-172018400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr2:172015200-172018400	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr2:172015200-172018400	Active TSS	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links