Variant report

Variant	rs4667659
Chromosome Location	chr2:171672858-171672859
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	POLR2A	chr2:171672750-171673716	K562	blood:	n/a	n/a
2	POLR2A	chr2:171669667-171676754	H1-neurons	neurons:	n/a	n/a
3	CTBP2	chr2:171672114-171675650	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr2:171672247-171673640	K562	blood:	n/a	n/a
5	SIN3A	chr2:171669186-171672942	H1-hESC	embryonic stem cell:	n/a	chr2:171670866-171670879 chr2:171672333-171672342 chr2:171670871-171670885 chr2:171672540-171672553
6	MAX	chr2:171672815-171674570	ECC-1	luminal epithelium:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
7	CTCF	chr2:171671323-171672998	SK-N-SH	brain:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672131-171672140 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
8	CTCF	chr2:171672740-171672890	HRE	kidney:	n/a	n/a
9	ZBTB7A	chr2:171672167-171673026	ECC-1	luminal epithelium:	n/a	chr2:171672569-171672576
10	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
11	NR2F2	chr2:171672171-171672982	K562	blood:	n/a	n/a
12	ZNF143	chr2:171672215-171672898	H1-hESC	embryonic stem cell:	n/a	n/a
13	SMC3	chr2:171672149-171672908	K562	blood:	n/a	chr2:171672411-171672425
14	RAD21	chr2:171672038-171673105	HCT-116	colon:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
15	ELF1	chr2:171672170-171672998	GM12878	blood:	n/a	n/a
16	RCOR1	chr2:171672232-171673647	K562	blood:	n/a	n/a
17	RUNX3	chr2:171672654-171673062	GM12878	blood:	n/a	n/a
18	CTCF	chr2:171672820-171672970	SK-N-SH_RA	brain:	n/a	n/a
19	CCNT2	chr2:171672247-171672908	K562	blood:	n/a	n/a
20	MAX	chr2:171672156-171674321	K562	blood:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
21	TEAD4	chr2:171672155-171672928	K562	blood:	n/a	n/a
22	RAD21	chr2:171671989-171672862	HCT-116	colon:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
23	MAZ	chr2:171672831-171673559	GM12878	blood:	n/a	n/a
24	REST	chr2:171671891-171674465	H1-neurons	neurons:	n/a	chr2:171672540-171672553
25	ZNF384	chr2:171672262-171673532	K562	blood:	n/a	n/a
26	POLR2A	chr2:171669237-171676101	H1-neurons	neurons:	n/a	n/a
27	RUNX3	chr2:171672631-171673050	GM12878	blood:	n/a	n/a
28	E2F6	chr2:171672809-171672957	K562	blood:	n/a	n/a
29	CTCF	chr2:171672720-171672870	Caco-2	colon:	n/a	n/a
30	CTCF	chr2:171672840-171672990	SAEC	small airway:	n/a	n/a
31	CTCF	chr2:171671973-171673050	A549	lung:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672131-171672140 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
32	CTCF	chr2:171671946-171673131	HCT-116	colon:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672131-171672140 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
33	MAZ	chr2:171672227-171674201	K562	blood:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
34	MAX	chr2:171672229-171674633	ECC-1	luminal epithelium:	n/a	chr2:171673743-171673753 chr2:171673740-171673750
35	ZNF263	chr2:171672009-171672943	HEK293-T-REx	kidney:	n/a	chr2:171672243-171672264

No.	Distal block	Cell Line	Cell type
1	chr2:171672439..171674320-chr2:171784947..171786968,2	K562	blood:
2	chr2:171672266..171672902-chr2:171785238..171786136,2	MCF-7	breast:
3	chr2:171671327..171674926-chr2:171677821..171681963,4	K562	blood:
4	chr2:171672408..171674860-chr2:171784778..171786781,3	MCF-7	breast:
5	chr2:171669367..171672253-chr2:171672351..171673917,2	K562	blood:
6	chr2:171671156..171674030-chr2:171674159..171676823,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC007405.2.1-3	chr2:171672813-171672995	ENSG00000235934.1
2	lnc-AC007405.2.1-3	chr2:171672803-171672995	ENSG00000235934.1

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16823157	0.85[AMR][1000 genomes]
rs17694726	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17700577	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17700773	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751683	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1894918	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2160414	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41393845	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45465192	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45471500	0.87[EUR][1000 genomes]
rs45473292	0.96[AMR][1000 genomes]
rs45486908	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45506192	0.87[EUR][1000 genomes]
rs45626540	0.87[EUR][1000 genomes]
rs4667653	0.89[AMR][1000 genomes]
rs4667654	0.89[AMR][1000 genomes]
rs4667655	0.85[AMR][1000 genomes]
rs4667660	0.83[AMR][1000 genomes]
rs4667661	0.87[EUR][1000 genomes]
rs4668307	0.85[AMR][1000 genomes]
rs4668310	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668311	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668318	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668319	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668322	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4668330	0.87[EUR][1000 genomes]
rs56852746	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs701491	0.87[EUR][1000 genomes]
rs769406	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171669600-171673000	Bivalent/Poised TSS	Fetal Brain Female	brain
2	chr2:171669600-171675400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr2:171670200-171676200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
4	chr2:171670400-171676600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:171671400-171675200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:171671400-171675400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:171671600-171673400	Enhancers	Pancreas	Pancrea
8	chr2:171671800-171675400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:171672000-171673000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:171672000-171673000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:171672000-171673000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
12	chr2:171672000-171673000	Bivalent Enhancer	Fetal Brain Male	brain
13	chr2:171672000-171673000	Flanking Active TSS	K562	blood
14	chr2:171672000-171673200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
15	chr2:171672000-171673200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
16	chr2:171672000-171673200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
17	chr2:171672000-171673200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr2:171672000-171673400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
19	chr2:171672000-171674600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
20	chr2:171672000-171674800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
21	chr2:171672000-171675200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
22	chr2:171672000-171675600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:171672200-171673000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
24	chr2:171672200-171673000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:171672200-171673000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:171672200-171673000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
27	chr2:171672200-171673000	Flanking Bivalent TSS/Enh	Right Ventricle	heart
28	chr2:171672200-171673000	Flanking Active TSS	GM12878-XiMat	blood
29	chr2:171672200-171673000	Bivalent Enhancer	NH-A	brain
30	chr2:171672200-171673200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:171672200-171673200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
34	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
37	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
38	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr2:171672200-171673200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr2:171672200-171673400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:171672200-171673400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:171672200-171673600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr2:171672200-171673800	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr2:171672200-171674000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:171672200-171674200	Bivalent Enhancer	Fetal Heart	heart
46	chr2:171672200-171674400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
47	chr2:171672200-171674600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:171672200-171675200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:171672200-171675400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr2:171672200-171675400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

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