Variant report

Variant	rs45473292
Chromosome Location	chr2:171678269-171678270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr2:171676326-171681103	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr2:171678236-171679635	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:171677005-171680495	H1-neurons	neurons:	n/a	n/a
4	SUZ12	chr2:171676388-171680031	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:171677825-171678334	H1-neurons	neurons:	n/a	n/a
6	GATA1	chr2:171677081-171680037	PBDE	blood:	n/a	chr2:171679713-171679722 chr2:171679319-171679327 chr2:171678862-171678872 chr2:171679660-171679673

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:171678251-171678301	HL-60	blood:	n/a
2	chr2:171678251-171678301	NHBE	bronchial:	n/a
3	chr2:171678251-171678301	Hepatocyte	liver:	n/a
4	chr2:171678251-171678301	HEK293	kidney:	embryo
5	chr2:171678251-171678301	AG10803	skin:	n/a
6	chr2:171678251-171678301	HIPEpiC	eye:	n/a
7	chr2:171678251-171678301	HRCEpiC	kidney:	n/a
8	chr2:171678251-171678301	RPTEC	kidney:	n/a
9	chr2:171678251-171678301	SK-N-MC	brain:	n/a
10	chr2:171678251-171678301	NHDF-neo	bronchial:	n/a
11	chr2:171678251-171678301	HCT-116	colon:	n/a
12	chr2:171678251-171678301	NB4	blood:	n/a
13	chr2:171678251-171678301	GM12892	blood:	n/a
14	chr2:171678251-171678301	GM12878	blood:	n/a
15	chr2:171678251-171678301	SK-N-SH_RA	brain:	n/a
16	chr2:171678251-171678301	A549	lung:	n/a
17	chr2:171678251-171678301	HRPEpiC	eye:	n/a
18	chr2:171678251-171678301	HEEpiC	esophagus:	n/a
19	chr2:171678251-171678301	AoSMC	blood vessel:	n/a
20	chr2:171678251-171678301	HPAEpiC	pulmonary alveolar:	n/a
21	chr2:171678251-171678301	GM19239	blood:	n/a
22	chr2:171678251-171678301	SAEC	small airway:	n/a
23	chr2:171678251-171678301	GM06990	blood:	n/a
24	chr2:171678251-171678301	HMEC	breast:	n/a
25	chr2:171678251-171678301	ProgFib	skin:	n/a
26	chr2:171678251-171678301	HAEpiC	amniotic membrane:	n/a
27	chr2:171678251-171678301	ovcar-3	ovarian:	n/a
28	chr2:171678251-171678301	Hela-S3	cervix:	n/a
29	chr2:171678251-171678301	SK-N-SH	brain:	n/a
30	chr2:171678251-171678301	HUVEC	blood vessel:	n/a
31	chr2:171678251-171678301	SKMC	muscle:	n/a
32	chr2:171678251-171678301	LNCaP	prostate:	n/a
33	chr2:171678251-171678301	AG04450	lung:	fetal
34	chr2:171678251-171678301	Jurkat	blood:	n/a
35	chr2:171678251-171678301	HNPCEpiC	eye:	n/a
36	chr2:171678251-171678301	BJ	skin:	n/a
37	chr2:171678251-171678301	CMK	blood:	n/a
38	chr2:171678251-171678301	H1-hESC	embryonic stem cell:	embryo
39	chr2:171678251-171678301	NH-A	brain:	n/a
40	chr2:171678251-171678301	K562	blood:	n/a
41	chr2:171678251-171678301	IMR90	lung:	fetal
42	chr2:171678251-171678301	U87	brain:	n/a
43	chr2:171678251-171678301	BE2_C	brain:	n/a
44	chr2:171678251-171678301	HRE	kidney:	n/a
45	chr2:171678251-171678301	GM12891	blood:	n/a
46	chr2:171678251-171678301	T-47D	breast:	n/a
47	chr2:171678251-171678301	HCF	heart:	n/a
48	chr2:171678251-171678301	AG09319	gingival:	n/a
49	chr2:171678251-171678301	HCPEpiC	choroid plexus:	n/a
50	chr2:171678251-171678301	AG09309	skin:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171671327..171674926-chr2:171677821..171681963,4	K562	blood:
2	chr2:171673426..171677773-chr2:171677821..171680534,5	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC007405.7.1-3	chr2:171678228-171678659	NONHSAT075433

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16823157	0.89[AMR][1000 genomes]
rs16858900	1.00[AFR][1000 genomes]
rs16858920	1.00[AFR][1000 genomes]
rs17694726	0.96[AMR][1000 genomes]
rs17700577	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs17700773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17751683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1894918	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2160414	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3791875	0.80[AMR][1000 genomes]
rs3791879	0.80[AMR][1000 genomes]
rs41393845	1.00[AMR][1000 genomes]
rs45465192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs45467694	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs45471500	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs45486908	1.00[AMR][1000 genomes]
rs45506192	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs45626540	0.81[AMR][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]
rs4667660	0.86[AMR][1000 genomes]
rs4667661	0.81[AMR][1000 genomes]
rs4668301	1.00[AFR][1000 genomes]
rs4668307	0.89[AMR][1000 genomes]
rs4668310	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4668311	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4668318	0.96[AMR][1000 genomes]
rs4668319	0.96[AMR][1000 genomes]
rs4668322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4668328	1.00[AFR][1000 genomes]
rs4668330	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs56852746	0.82[AMR][1000 genomes]
rs701491	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs769406	0.81[AMR][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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171674400-171682200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:171676200-171679400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
3	chr2:171676400-171679000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
4	chr2:171676400-171679000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
5	chr2:171676400-171679200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr2:171676400-171679400	Bivalent Enhancer	Fetal Thymus	thymus
7	chr2:171676400-171679600	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr2:171676400-171679800	Bivalent Enhancer	Fetal Stomach	stomach
9	chr2:171676600-171679400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
10	chr2:171676600-171679400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
11	chr2:171676800-171678400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:171676800-171678400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
13	chr2:171676800-171678800	Flanking Active TSS	Right Ventricle	heart
14	chr2:171676800-171679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:171676800-171679200	Bivalent Enhancer	Lung	lung
16	chr2:171676800-171679600	Enhancers	Gastric	stomach
17	chr2:171676800-171679800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr2:171676800-171680000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
19	chr2:171676800-171680600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:171676800-171680600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
21	chr2:171676800-171681200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
22	chr2:171677000-171679800	Bivalent Enhancer	Esophagus	oesophagus
23	chr2:171677000-171680000	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr2:171677200-171678600	Active TSS	Right Atrium	heart
25	chr2:171677200-171679000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr2:171677200-171680600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr2:171677400-171679200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:171677400-171680000	Bivalent Enhancer	Fetal Lung	lung
29	chr2:171677400-171680600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr2:171677600-171678400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:171677600-171679000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
32	chr2:171677600-171679200	Bivalent Enhancer	Spleen	Spleen
33	chr2:171677600-171679400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr2:171677600-171679400	Bivalent Enhancer	Fetal Brain Male	brain
35	chr2:171677600-171679600	Bivalent Enhancer	Left Ventricle	heart
36	chr2:171677600-171680600	Bivalent Enhancer	Placenta	Placenta
37	chr2:171677800-171678400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
38	chr2:171677800-171678400	Bivalent/Poised TSS	HSMMtube	muscle
39	chr2:171677800-171678800	Bivalent Enhancer	Colon Smooth Muscle	Colon
40	chr2:171677800-171679000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr2:171677800-171679000	Bivalent Enhancer	Colonic Mucosa	Colon
42	chr2:171677800-171679200	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr2:171677800-171679200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
44	chr2:171677800-171679800	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr2:171677800-171679800	Bivalent Enhancer	HMEC	breast
46	chr2:171677800-171679800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr2:171677800-171680000	Enhancers	Pancreas	Pancrea
48	chr2:171677800-171680400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:171677800-171680600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
50	chr2:171677800-171680600	Bivalent Enhancer	Liver	Liver

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