Variant report

Variant	rs7563812
Chromosome Location	chr2:171570488-171570489
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	HMGN3	chr2:171570229-171571461	K562	blood:	n/a	n/a
2	POLR2A	chr2:171570478-171570524	K562	blood:	n/a	n/a
3	RCOR1	chr2:171569680-171570544	HepG2	liver:	n/a	n/a
4	MAX	chr2:171567494-171574371	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
5	POLR2A	chr2:171569736-171570695	HepG2	liver:	n/a	n/a
6	CHD2	chr2:171569669-171572660	HepG2	liver:	n/a	n/a
7	CBX3	chr2:171570404-171572616	K562	blood:	n/a	n/a
8	POLR2A	chr2:171566521-171571156	HepG2	liver:	n/a	n/a
9	MAX	chr2:171567137-171574353	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
10	MYBL2	chr2:171566484-171570541	HepG2	liver:	n/a	n/a
11	HEY1	chr2:171566552-171576261	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
12	MYBL2	chr2:171569644-171570562	HepG2	liver:	n/a	n/a
13	HEY1	chr2:171566435-171575595	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
14	POLR2A	chr2:171567948-171571413	HepG2	liver:	n/a	n/a
15	SETDB1	chr2:171569664-171571382	K562	blood:	n/a	n/a
16	CCNT2	chr2:171569996-171570591	K562	blood:	n/a	n/a
17	POLR2A	chr2:171566818-171576833	HepG2	liver:	n/a	n/a
18	CREB1	chr2:171567131-171573329	HepG2	liver:	n/a	n/a
19	TAF1	chr2:171569826-171570693	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:171567743-171574223	HepG2	liver:	n/a	n/a
21	MAX	chr2:171570240-171572530	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100
22	TAF1	chr2:171569511-171571441	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:171566596-171571451	HepG2	liver:	n/a	n/a
24	SUZ12	chr2:171568999-171573118	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:171566701-171575246	HepG2	liver:	n/a	n/a
26	SREBP1	chr2:171570439-171572513	HepG2	liver:	n/a	n/a
27	CTBP2	chr2:171567955-171571219	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr2:171569523-171571384	HepG2	liver:	n/a	n/a
29	E2F6	chr2:171570290-171571067	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr2:171569767-171570668	HepG2	liver:	n/a	n/a
31	E2F6	chr2:171570248-171570849	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171568787..171573894-chr2:171626202..171629385,10	K562	blood:
2	chr2:171570330..171572699-chr2:171627295..171629894,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC007405.2.1-1	chr2:171568949-171571077	NR_027433

Variant related genes	Relation type
SP5	TF binding region
ENSG00000239467	Chromatin interaction
ENSG00000234350	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10179149	0.89[ASN][1000 genomes]
rs10181981	0.89[ASN][1000 genomes]
rs10184230	0.87[ASN][1000 genomes]
rs10185519	0.89[ASN][1000 genomes]
rs10188135	0.89[ASN][1000 genomes]
rs10193894	0.89[ASN][1000 genomes]
rs10200830	0.89[ASN][1000 genomes]
rs10204585	0.87[ASN][1000 genomes]
rs10211629	0.89[ASN][1000 genomes]
rs10460355	0.80[ASN][1000 genomes]
rs10460356	0.82[ASN][1000 genomes]
rs10930437	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472667	0.82[ASN][1000 genomes]
rs12611849	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614245	0.90[ASN][1000 genomes]
rs12618173	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12990209	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12994080	0.87[ASN][1000 genomes]
rs13009323	0.82[ASN][1000 genomes]
rs13015956	0.89[ASN][1000 genomes]
rs1362487	0.80[ASN][1000 genomes]
rs1362491	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1420377	0.82[ASN][1000 genomes]
rs1420382	0.93[ASN][1000 genomes]
rs1420384	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1477060	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17694506	0.82[ASN][1000 genomes]
rs17750734	0.87[ASN][1000 genomes]
rs1861463	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894917	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2058726	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2216135	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287109	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356232	0.93[ASN][1000 genomes]
rs2883885	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28863322	0.82[ASN][1000 genomes]
rs28892917	0.82[ASN][1000 genomes]
rs35294186	0.89[ASN][1000 genomes]
rs4233832	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667649	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667650	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4667651	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667652	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4667658	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4668302	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668303	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668304	0.93[ASN][1000 genomes]
rs4668305	0.93[ASN][1000 genomes]
rs4668306	0.93[ASN][1000 genomes]
rs4668312	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668314	0.82[ASN][1000 genomes]
rs5003926	0.92[ASN][1000 genomes]
rs5003927	0.93[ASN][1000 genomes]
rs55806232	0.87[ASN][1000 genomes]
rs58691943	0.89[ASN][1000 genomes]
rs6433236	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6433237	0.92[ASN][1000 genomes]
rs6433239	0.93[ASN][1000 genomes]
rs6433240	0.93[ASN][1000 genomes]
rs6433242	0.90[ASN][1000 genomes]
rs6433243	0.87[ASN][1000 genomes]
rs6433245	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs66624589	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6717778	0.93[ASN][1000 genomes]
rs6717785	0.93[ASN][1000 genomes]
rs6726174	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6727988	0.89[ASN][1000 genomes]
rs6732964	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741549	0.90[ASN][1000 genomes]
rs6746220	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746374	0.82[ASN][1000 genomes]
rs6751667	0.80[ASN][1000 genomes]
rs6751987	0.80[AMR][1000 genomes]
rs6756891	0.89[ASN][1000 genomes]
rs7556674	0.89[ASN][1000 genomes]
rs7572599	0.93[ASN][1000 genomes]
rs7582102	0.93[ASN][1000 genomes]
rs7582425	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7582430	0.89[ASN][1000 genomes]
rs7594247	0.90[ASN][1000 genomes]
rs7595158	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7608898	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs959463	0.93[ASN][1000 genomes]
rs959464	0.93[ASN][1000 genomes]
rs959465	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875409	chr2:171565376-171577859	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv821786	chr2:171567780-171574707	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv583609	chr2:171568633-171573309	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583610	chr2:171568633-171573529	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15608	chr2:171569890-171574062	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7563812	AC007405.4	cis	Stomach	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171568000-171571600	Bivalent Enhancer	Fetal Brain Male	brain
2	chr2:171568200-171570600	Bivalent Enhancer	Fetal Stomach	stomach
3	chr2:171568400-171570600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr2:171568400-171570600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr2:171568400-171571400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:171568600-171570600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
7	chr2:171568600-171570600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr2:171568800-171570600	Bivalent Enhancer	Fetal Brain Female	brain
9	chr2:171568800-171570600	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr2:171568800-171570800	Bivalent Enhancer	Fetal Lung	lung
11	chr2:171569000-171570800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
12	chr2:171569000-171570800	Bivalent Enhancer	Fetal Thymus	thymus
13	chr2:171569200-171573000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr2:171569400-171570600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr2:171569400-171574400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:171569600-171571400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:171569600-171571600	Bivalent Enhancer	Spleen	Spleen
18	chr2:171569600-171574800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:171569600-171575600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:171569800-171570600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:171569800-171570600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
22	chr2:171569800-171570600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
23	chr2:171569800-171570600	Bivalent Enhancer	Placenta	Placenta
24	chr2:171569800-171571000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:171569800-171571000	Bivalent/Poised TSS	Thymus	Thymus
26	chr2:171569800-171572400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:171569800-171572600	Flanking Active TSS	Liver	Liver
28	chr2:171570000-171570600	Flanking Active TSS	Lung	lung
29	chr2:171570000-171570800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:171570000-171570800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
31	chr2:171570000-171570800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:171570000-171570800	Flanking Active TSS	Gastric	stomach
33	chr2:171570000-171570800	Flanking Active TSS	Pancreas	Pancrea
34	chr2:171570000-171570800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
35	chr2:171570000-171571200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
36	chr2:171570000-171571800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:171570000-171572600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:171570000-171572600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr2:171570000-171572600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
40	chr2:171570000-171572600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
41	chr2:171570000-171573200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:171570000-171574000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
43	chr2:171570000-171575600	Bivalent/Poised TSS	HepG2	liver
44	chr2:171570000-171576200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr2:171570200-171570600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
46	chr2:171570200-171570600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
47	chr2:171570200-171570600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
48	chr2:171570200-171570600	Bivalent Enhancer	Ovary	ovary
49	chr2:171570200-171570600	Flanking Active TSS	Right Atrium	heart
50	chr2:171570200-171571000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell

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