Variant report

Variant	rs45486908
Chromosome Location	chr2:171673464-171673465
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	CTCF	chr2:171673340-171673490	WERI-Rb-1	eye:	n/a	n/a
2	MTA3	chr2:171673330-171673716	GM12878	blood:	n/a	n/a
3	RAD21	chr2:171673306-171673488	Hela-S3	cervix:	n/a	n/a
4	HCFC1	chr2:171673384-171673604	K562	blood:	n/a	n/a
5	MAX	chr2:171673302-171673603	A549	lung:	n/a	n/a
6	BACH1	chr2:171673461-171673478	K562	blood:	n/a	n/a
7	HDAC2	chr2:171673275-171673591	K562	blood:	n/a	n/a
8	POLR2A	chr2:171672750-171673716	K562	blood:	n/a	n/a
9	POLR2A	chr2:171673176-171673782	MCF-7	breast:	n/a	n/a
10	ZBTB7A	chr2:171673133-171674569	ECC-1	luminal epithelium:	n/a	n/a
11	CHD2	chr2:171673226-171673605	K562	blood:	n/a	n/a
12	MAX	chr2:171673232-171673745	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:171673082-171673671	U87	brain:	n/a	n/a
14	POLR2A	chr2:171669667-171676754	H1-neurons	neurons:	n/a	n/a
15	SIN3AK20	chr2:171673297-171673552	PANC-1	pancreas:	n/a	n/a
16	TCF12	chr2:171673280-171673620	GM12878	blood:	n/a	n/a
17	MAX	chr2:171673111-171673780	MCF-7	breast:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
18	POLR2A	chr2:171673232-171673651	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr2:171673442-171673476	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:171673042-171673677	U87	brain:	n/a	n/a
21	MAX	chr2:171673081-171673967	A549	lung:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
22	CHD2	chr2:171673366-171673517	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr2:171673323-171673595	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr2:171673158-171673586	NB4	blood:	n/a	n/a
25	EGR1	chr2:171673128-171673553	K562	blood:	n/a	chr2:171673289-171673299
26	RCOR1	chr2:171673192-171673556	Hela-S3	cervix:	n/a	n/a
27	CTBP2	chr2:171672114-171675650	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr2:171673420-171673520	HUVEC	blood vessel:	n/a	n/a
29	CHD2	chr2:171673166-171673604	Hela-S3	cervix:	n/a	n/a
30	MYC	chr2:171672247-171673640	K562	blood:	n/a	n/a
31	ELF1	chr2:171673147-171673725	MCF-7	breast:	n/a	chr2:171673435-171673448
32	ZNF263	chr2:171673237-171673677	HEK293-T-REx	kidney:	n/a	n/a
33	MXI1	chr2:171673271-171673594	GM12878	blood:	n/a	n/a
34	HDAC2	chr2:171673155-171673735	MCF-7	breast:	n/a	chr2:171673179-171673193 chr2:171673180-171673194
35	EBF1	chr2:171673316-171673659	GM12878	blood:	n/a	n/a
36	CTCF	chr2:171673447-171673518	MCF-7	breast:	n/a	n/a
37	E2F6	chr2:171673229-171673788	H1-hESC	embryonic stem cell:	n/a	chr2:171673522-171673533 chr2:171673335-171673344 chr2:171673289-171673299 chr2:171673745-171673754 chr2:171673274-171673283
38	MAX	chr2:171672815-171674570	ECC-1	luminal epithelium:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
39	MAX	chr2:171672946-171673620	K562	blood:	n/a	n/a
40	UBTF	chr2:171673191-171674325	K562	blood:	n/a	n/a
41	ELF1	chr2:171673207-171673562	K562	blood:	n/a	chr2:171673435-171673448
42	SMC3	chr2:171673182-171673565	Hela-S3	cervix:	n/a	n/a
43	REST	chr2:171673165-171673518	K562	blood:	n/a	n/a
44	E2F6	chr2:171673168-171673577	K562	blood:	n/a	chr2:171673522-171673533 chr2:171673335-171673344 chr2:171673289-171673299 chr2:171673274-171673283
45	MYC	chr2:171673252-171673592	MCF-7	breast:	n/a	n/a
46	BRCA1	chr2:171673162-171673500	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr2:171673255-171673691	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:171673240-171673612	MCF-7	breast:	n/a	n/a
49	ZMIZ1	chr2:171673411-171673583	K562	blood:	n/a	n/a
50	TEAD4	chr2:171672991-171673584	K562	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	chr2:171669367..171672253-chr2:171672351..171673917,2	K562	blood:
5	chr2:171671156..171674030-chr2:171674159..171676823,3	K562	blood:
6	chr2:171673426..171677773-chr2:171677821..171680534,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC007405.2.1-3	chr2:171673364-171673542	ENSG00000235934.1
2	lnc-AC007405.2.1-3	chr2:171673364-171673509	ENSG00000235934.1
3	lnc-AC007405.2.1-3	chr2:171673364-171673682	ENSG00000235934.1

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs16823157	0.89[AMR][1000 genomes]
rs17694726	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17700577	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17700773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751683	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1894918	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2160414	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3791875	0.80[AMR][1000 genomes]
rs3791879	0.80[AMR][1000 genomes]
rs41393845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45465192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45467694	0.81[AMR][1000 genomes]
rs45471500	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs45473292	1.00[AMR][1000 genomes]
rs45506192	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs45626540	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4667653	0.92[AMR][1000 genomes]
rs4667654	0.92[AMR][1000 genomes]
rs4667655	0.89[AMR][1000 genomes]
rs4667659	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4667660	0.86[AMR][1000 genomes]
rs4667661	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4668307	0.89[AMR][1000 genomes]
rs4668310	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668311	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668318	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668319	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4668330	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56852746	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs701491	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs769406	0.81[AMR][1000 genomes];0.87[EUR][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:125 , 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	chr2:171672200-171673600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
12	chr2:171672200-171673800	Flanking Bivalent TSS/Enh	HepG2	liver
13	chr2:171672200-171674000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:171672200-171674200	Bivalent Enhancer	Fetal Heart	heart
15	chr2:171672200-171674400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
16	chr2:171672200-171674600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:171672200-171675200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:171672200-171675400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:171672200-171675400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:171672400-171673800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
21	chr2:171672400-171674200	Bivalent Enhancer	Fetal Lung	lung
22	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
23	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
24	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
25	chr2:171672400-171674400	Flanking Bivalent TSS/Enh	Placenta	Placenta
26	chr2:171672400-171674600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr2:171672400-171674600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr2:171672400-171675400	Active TSS	Aorta	Aorta
29	chr2:171672400-171675600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:171672400-171675600	Bivalent Enhancer	Spleen	Spleen
31	chr2:171672400-171676400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:171672600-171673800	Bivalent/Poised TSS	Osteobl	bone
33	chr2:171672600-171674000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:171672600-171674600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
35	chr2:171672800-171673600	Bivalent Enhancer	Small Intestine	intestine
36	chr2:171672800-171673800	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr2:171672800-171673800	Active TSS	Ovary	ovary
38	chr2:171672800-171673800	Bivalent Enhancer	Stomach Mucosa	stomach
39	chr2:171672800-171674200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr2:171672800-171674600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr2:171672800-171675200	Bivalent/Poised TSS	NHLF	lung
42	chr2:171673000-171673800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:171673000-171673800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr2:171673000-171673800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:171673000-171673800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:171673000-171673800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:171673000-171673800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:171673000-171673800	Bivalent/Poised TSS	HMEC	breast
49	chr2:171673000-171673800	Active TSS	NHEK	skin
50	chr2:171673000-171674000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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