Variant report

Variant	rs1768672
Chromosome Location	chr1:220165013-220165014
allele	A/C
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	GATA1	chr1:220164695-220165723	PBDE	blood:	n/a	n/a
2	POLR2A	chr1:220165006-220165693	HepG2	liver:	n/a	n/a
3	CTCF	chr1:220164043-220165084	SK-N-SH	brain:	n/a	chr1:220164526-220164547 chr1:220164529-220164537 chr1:220164524-220164542
4	CTCF	chr1:220164104-220165175	A549	lung:	n/a	chr1:220164526-220164547 chr1:220164529-220164537 chr1:220164524-220164542
5	POLR2A	chr1:220161313-220168073	K562	blood:	n/a	n/a
6	RAD21	chr1:220164166-220165365	SK-N-SH	brain:	n/a	chr1:220164527-220164534 chr1:220164525-220164544

No.	Distal block	Cell Line	Cell type
1	chr1:220153591..220159773-chr1:220159981..220165102,9	K562	blood:
2	chr1:220164810..220167759-chr1:220168424..220170636,2	K562	blood:
3	chr1:220163102..220165191-chr1:220201695..220204471,2	K562	blood:
4	chr1:220049633..220050383-chr1:220164327..220165162,2	MCF-7	breast:
5	chr1:220144163..220148221-chr1:220163054..220166012,3	K562	blood:
6	chr1:220163484..220165362-chr1:220165481..220167153,2	K562	blood:
7	chr1:220163115..220165079-chr1:220292412..220294107,2	K562	blood:
8	chr1:220072242..220074837-chr1:220162775..220165302,2	K562	blood:
9	chr1:220011035..220013766-chr1:220162762..220165197,2	K562	blood:

Variant related genes	Relation type
ENSG00000238798	TF binding region
ENSG00000136628	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10442691	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10863527	0.86[ASN][1000 genomes]
rs10863528	0.86[ASN][1000 genomes]
rs12140664	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1630386	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1694575	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1694577	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1694601	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1768666	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1768668	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1768673	0.87[ASN][1000 genomes]
rs1768675	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2254494	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2454326	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2486328	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2577137	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2577162	0.86[ASN][1000 genomes]
rs2577164	0.86[ASN][1000 genomes]
rs2647425	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2647435	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2647436	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2647453	0.85[ASN][1000 genomes]
rs2647459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647460	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2647468	0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2789796	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2789798	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789799	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv998124	chr1:220132739-220189211	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
3	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
4	esv1798515	chr1:220157811-220167371	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220132800-220177000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220140000-220167400	Weak transcription	Gastric	stomach
3	chr1:220140800-220173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
6	chr1:220141400-220165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:220142600-220169400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:220146400-220182800	Weak transcription	Spleen	Spleen
9	chr1:220147200-220169400	Weak transcription	Fetal Heart	heart
10	chr1:220149000-220167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:220149400-220178200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:220149600-220166800	Weak transcription	Stomach Mucosa	stomach
13	chr1:220153600-220169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:220154200-220169200	Weak transcription	Fetal Brain Male	brain
15	chr1:220154400-220169200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:220154400-220169200	Weak transcription	Fetal Lung	lung
17	chr1:220154600-220166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:220154600-220167000	Weak transcription	Aorta	Aorta
19	chr1:220154600-220169000	Weak transcription	Small Intestine	intestine
20	chr1:220154600-220169200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:220154800-220167400	Weak transcription	Pancreas	Pancrea
22	chr1:220155000-220166000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:220155600-220168600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:220156800-220169800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:220157000-220168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:220157200-220167000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:220157200-220177200	Weak transcription	Esophagus	oesophagus
28	chr1:220158200-220166000	Weak transcription	Lung	lung
29	chr1:220158200-220167200	Weak transcription	Ovary	ovary
30	chr1:220158200-220177200	Weak transcription	Right Ventricle	heart
31	chr1:220159200-220166200	Weak transcription	Fetal Stomach	stomach
32	chr1:220159200-220168800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:220159800-220169200	Weak transcription	Colonic Mucosa	Colon
34	chr1:220160200-220168600	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:220160400-220167400	Weak transcription	Primary B cells from cord blood	blood
36	chr1:220160400-220168600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:220160600-220167000	Enhancers	Liver	Liver
38	chr1:220160800-220166000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:220160800-220169200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:220160800-220174200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:220161000-220165400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:220161000-220167400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:220161000-220168800	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:220161000-220168800	Weak transcription	Thymus	Thymus
45	chr1:220161000-220169200	Weak transcription	Psoas Muscle	Psoas
46	chr1:220161000-220169200	Weak transcription	NHLF	lung
47	chr1:220161200-220166600	Weak transcription	Fetal Brain Female	brain
48	chr1:220161200-220168800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:220161200-220169200	Weak transcription	Left Ventricle	heart
50	chr1:220161600-220168800	Weak transcription	Primary hematopoietic stem cells	blood

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