Variant report

Variant	rs3762553
Chromosome Location	chr2:171674098-171674099
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	GABPA	chr2:171673812-171674357	H1-hESC	embryonic stem cell:	n/a	chr2:171674114-171674128 chr2:171673988-171673997 chr2:171673986-171673995
2	ZBTB7A	chr2:171673133-171674569	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr2:171669667-171676754	H1-neurons	neurons:	n/a	n/a
4	YY1	chr2:171673884-171674210	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:171673881-171674167	ProgFib	skin:	n/a	n/a
6	CTCF	chr2:171674080-171674230	NHEK	skin:	n/a	chr2:171674164-171674177
7	ZNF263	chr2:171673949-171674561	HEK293-T-REx	kidney:	n/a	n/a
8	CTBP2	chr2:171672114-171675650	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr2:171672815-171674570	ECC-1	luminal epithelium:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
10	UBTF	chr2:171673191-171674325	K562	blood:	n/a	n/a
11	YY1	chr2:171673974-171674259	GM12878	blood:	n/a	n/a
12	MAX	chr2:171673841-171674303	Hela-S3	cervix:	n/a	n/a
13	MAX	chr2:171674039-171674167	GM12878	blood:	n/a	n/a
14	TEAD4	chr2:171674081-171674372	H1-hESC	embryonic stem cell:	n/a	n/a
15	YY1	chr2:171673821-171674313	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr2:171673031-171674152	A549	lung:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
17	SIN3AK20	chr2:171673734-171674324	PANC-1	pancreas:	n/a	n/a
18	YY1	chr2:171673906-171674189	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:171673927-171674127	Hela-S3	cervix:	n/a	n/a
20	E2F6	chr2:171672306-171674313	K562	blood:	n/a	chr2:171673522-171673533 chr2:171673335-171673344 chr2:171673289-171673299 chr2:171672681-171672692 chr2:171672406-171672414 chr2:171673745-171673754 chr2:171673274-171673283 chr2:171672537-171672546
21	E2F6	chr2:171672968-171674451	H1-hESC	embryonic stem cell:	n/a	chr2:171673522-171673533 chr2:171673335-171673344 chr2:171673289-171673299 chr2:171673745-171673754 chr2:171673274-171673283
22	SUZ12	chr2:171673406-171675580	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZBTB7A	chr2:171673816-171674791	ECC-1	luminal epithelium:	n/a	n/a
24	E2F6	chr2:171673151-171674218	K562	blood:	n/a	chr2:171673522-171673533 chr2:171673335-171673344 chr2:171673289-171673299 chr2:171673745-171673754 chr2:171673274-171673283
25	MAX	chr2:171672156-171674321	K562	blood:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
26	HDAC2	chr2:171673931-171674272	HepG2	liver:	n/a	chr2:171673985-171673994
27	CTCF	chr2:171674000-171674150	AG10803	skin:	n/a	n/a
28	REST	chr2:171671891-171674465	H1-neurons	neurons:	n/a	chr2:171672540-171672553
29	POLR2A	chr2:171669237-171676101	H1-neurons	neurons:	n/a	n/a
30	MTA3	chr2:171674008-171674419	GM12878	blood:	n/a	n/a
31	HMGN3	chr2:171673944-171674187	K562	blood:	n/a	n/a
32	YY1	chr2:171673998-171674202	K562	blood:	n/a	n/a
33	MAZ	chr2:171672227-171674201	K562	blood:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
34	YY1	chr2:171673774-171674206	K562	blood:	n/a	n/a
35	E2F6	chr2:171673745-171674306	A549	lung:	n/a	chr2:171673745-171673754
36	MAX	chr2:171672229-171674633	ECC-1	luminal epithelium:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
37	POLR2A	chr2:171673071-171674546	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:171672439..171674320-chr2:171784947..171786968,2	K562	blood:
2	chr2:171671327..171674926-chr2:171677821..171681963,4	K562	blood:
3	chr2:171672408..171674860-chr2:171784778..171786781,3	MCF-7	breast:
4	chr2:171673426..171677773-chr2:171677821..171680534,5	K562	blood:

Variant related genes	Relation type
GAD1	TF binding region
ENSG00000235934	TF binding region
ENSG00000128683	Chromatin interaction
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1978340	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2356236	0.88[EUR][1000 genomes]
rs2883888	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34137349	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127716	0.82[AMR][1000 genomes]
rs3762556	0.88[EUR][1000 genomes]
rs3791871	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3791872	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3791878	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56989102	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62168446	0.82[AMR][1000 genomes]
rs62168448	0.82[AMR][1000 genomes]
rs62168454	0.99[ASN][1000 genomes]
rs6755814	0.81[ASN][1000 genomes]

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	esv1806894	chr2:171651783-171679041	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv528929	chr2:171672191-171678379	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171669600-171675400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr2:171670200-171676200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
3	chr2:171670400-171676600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:171671400-171675200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:171671400-171675400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:171671800-171675400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:171672000-171674600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
8	chr2:171672000-171674800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
9	chr2:171672000-171675200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
10	chr2:171672000-171675600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:171672200-171674200	Bivalent Enhancer	Fetal Heart	heart
12	chr2:171672200-171674400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
13	chr2:171672200-171674600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:171672200-171675200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:171672200-171675400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:171672200-171675400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:171672400-171674200	Bivalent Enhancer	Fetal Lung	lung
18	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
19	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
20	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Placenta	Placenta
22	chr2:171672400-171674600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
23	chr2:171672400-171674600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr2:171672400-171675400	Active TSS	Aorta	Aorta
25	chr2:171672400-171675600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:171672400-171675600	Bivalent Enhancer	Spleen	Spleen
27	chr2:171672400-171676400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:171672600-171674600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
29	chr2:171672800-171674200	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr2:171672800-171674600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr2:171672800-171675200	Bivalent/Poised TSS	NHLF	lung
32	chr2:171673000-171674200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:171673000-171674200	Active TSS	GM12878-XiMat	blood
34	chr2:171673000-171674200	Active TSS	HSMMtube	muscle
35	chr2:171673000-171674600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
36	chr2:171673000-171674600	Active TSS	K562	blood
37	chr2:171673000-171674800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
38	chr2:171673000-171675000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:171673000-171675000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr2:171673000-171675200	Active TSS	NHDF-Ad	bronchial
41	chr2:171673000-171675600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr2:171673000-171675600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
43	chr2:171673000-171675600	Bivalent/Poised TSS	HSMM	muscle
44	chr2:171673000-171676200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr2:171673200-171674200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:171673200-171674200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
47	chr2:171673200-171674400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:171673200-171674400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:171673200-171674600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:171673200-171674600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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