Variant report

Variant	rs1821968
Chromosome Location	chr2:111880623-111880624
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	TCF12	chr2:111880520-111880955	A549	lung:	n/a	n/a
2	POLR2A	chr2:111879663-111881213	HepG2	liver:	n/a	n/a
3	MAX	chr2:111877563-111881015	NB4	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
4	MAZ	chr2:111879727-111881042	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr2:111879914-111880972	Hela-S3	cervix:	n/a	n/a
6	CREB1	chr2:111880242-111881053	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3AK20	chr2:111877611-111881217	MCF-7	breast:	n/a	n/a
8	CHD1	chr2:111878621-111881270	H1-hESC	embryonic stem cell:	n/a	chr2:111878901-111878911
9	ZNF143	chr2:111879571-111880980	H1-hESC	embryonic stem cell:	n/a	chr2:111880343-111880353
10	POLR2A	chr2:111879821-111880936	HepG2	liver:	n/a	n/a
11	SMC3	chr2:111880460-111881083	Hela-S3	cervix:	n/a	n/a
12	HCFC1	chr2:111877979-111880854	K562	blood:	n/a	n/a
13	ATF2	chr2:111880539-111880933	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr2:111877942-111881067	IMR90	lung:	n/a	n/a
15	E2F1	chr2:111879848-111880927	Hela-S3	cervix:	n/a	chr2:111880549-111880558 chr2:111880095-111880104 chr2:111880318-111880330 chr2:111880053-111880060
16	MAX	chr2:111877542-111881163	HepG2	liver:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
17	ZNF384	chr2:111880538-111880822	K562	blood:	n/a	n/a
18	POLR2A	chr2:111877432-111881054	K562	blood:	n/a	n/a
19	SIN3AK20	chr2:111880591-111881055	SK-N-SH	brain:	n/a	n/a
20	MAZ	chr2:111879931-111880729	GM12878	blood:	n/a	n/a
21	MAFK	chr2:111880481-111881394	HepG2	liver:	n/a	chr2:111880845-111880856 chr2:111880844-111880855 chr2:111880836-111880853 chr2:111880845-111880856 chr2:111880844-111880855
22	BRCA1	chr2:111880441-111880867	Hela-S3	cervix:	n/a	n/a
23	SMARCB1	chr2:111877080-111881031	Hela-S3	cervix:	n/a	n/a
24	CHD2	chr2:111880566-111881006	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:111877652-111881216	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr2:111880604-111881074	H1-hESC	embryonic stem cell:	n/a	chr2:111880627-111880636 chr2:111880624-111880635
27	UBTF	chr2:111879632-111881100	K562	blood:	n/a	n/a
28	MYC	chr2:111877906-111880742	K562	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
29	RCOR1	chr2:111879101-111881089	K562	blood:	n/a	n/a
30	FOXP2	chr2:111880430-111881034	PFSK-1	brain:	n/a	n/a
31	MAFK	chr2:111880338-111881393	IMR90	lung:	n/a	chr2:111880845-111880856 chr2:111880844-111880855 chr2:111880836-111880853 chr2:111880845-111880856 chr2:111880844-111880855
32	E2F6	chr2:111877723-111880882	Hela-S3	cervix:	n/a	chr2:111878414-111878423 chr2:111880549-111880558 chr2:111880095-111880104 chr2:111877747-111877759 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111880318-111880330 chr2:111878285-111878294 chr2:111878171-111878181 chr2:111880053-111880060
33	CTCF	chr2:111880370-111880805	K562	blood:	n/a	n/a
34	E2F6	chr2:111879444-111880958	K562	blood:	n/a	chr2:111880549-111880558 chr2:111880095-111880104 chr2:111880318-111880330 chr2:111880053-111880060
35	UBTF	chr2:111877688-111881146	K562	blood:	n/a	n/a
36	MAFK	chr2:111880443-111881375	Hela-S3	cervix:	n/a	chr2:111880845-111880856 chr2:111880844-111880855 chr2:111880836-111880853 chr2:111880845-111880856 chr2:111880844-111880855
37	MXI1	chr2:111877406-111881885	SK-N-SH	brain:	n/a	n/a
38	USF2	chr2:111880532-111880714	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr2:111879687-111880987	H1-neurons	neurons:	n/a	n/a
40	JUND	chr2:111880411-111881013	H1-hESC	embryonic stem cell:	n/a	chr2:111880973-111880985
41	ZBTB7A	chr2:111880179-111880903	ECC-1	luminal epithelium:	n/a	chr2:111880410-111880419
42	BHLHE40	chr2:111877526-111880906	K562	blood:	n/a	chr2:111878164-111878180 chr2:111878158-111878174 chr2:111879083-111879099 chr2:111878389-111878405 chr2:111880077-111880093 chr2:111878166-111878182 chr2:111879143-111879159
43	SIN3AK20	chr2:111877950-111881096	PANC-1	pancreas:	n/a	n/a
44	TAF7	chr2:111880466-111881055	H1-hESC	embryonic stem cell:	n/a	n/a
45	HA-E2F1	chr2:111879917-111880930	Hela-S3	cervix:	n/a	chr2:111880549-111880558 chr2:111880095-111880104 chr2:111880318-111880330 chr2:111880053-111880060
46	CTBP2	chr2:111874524-111881050	H1-hESC	embryonic stem cell:	n/a	n/a
47	HEY1	chr2:111879624-111881075	HepG2	liver:	n/a	chr2:111879845-111879860 chr2:111880435-111880450
48	POLR2A	chr2:111877766-111881072	H1-hESC	embryonic stem cell:	n/a	n/a
49	GABPA	chr2:111880280-111880687	K562	blood:	n/a	n/a
50	CEBPB	chr2:111879621-111881073	Hela-S3	cervix:	n/a	chr2:111880095-111880103

No.	Distal block	Cell Line	Cell type
1	chr11:75273124..75273774-chr2:111879874..111880766,2	NB4	blood:
2	chr2:111434111..111436826-chr2:111878321..111880919,2	K562	blood:
3	chr2:111880097..111880707-chr6:33239744..33240317,2	HCT-116	colon:

Variant related genes	Relation type
BCL2L11	TF binding region
ENSG00000169679	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000149257	Chromatin interaction
ENSG00000223501	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10166773	0.86[JPT][hapmap]
rs10189015	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10211562	0.86[ASN][1000 genomes]
rs1054873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11674517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13398360	0.86[JPT][hapmap]
rs1439287	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837368	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241841	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789061	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789064	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789065	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789068	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4302219	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4627572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849403	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56952027	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60286362	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs616130	0.81[TSI][hapmap]
rs6708784	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6726007	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs6732491	0.86[JPT][hapmap]
rs6734942	0.92[ASN][1000 genomes]
rs6760053	0.90[JPT][hapmap]
rs7577824	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7593638	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7602904	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv829618	chr2:111875627-111881547	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv3392605	chr2:111879306-111881854	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1821968	SULT1C2	cis	cerebellum	SCAN
rs1821968	BCL2L11	cis	cerebellum	SCAN
rs1821968	DPP10	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111875600-111881200	Active TSS	Psoas Muscle	Psoas
2	chr2:111877000-111881000	Active TSS	Small Intestine	intestine
3	chr2:111877000-111881400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:111877200-111880800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:111877600-111881000	Active TSS	Esophagus	oesophagus
6	chr2:111877600-111881200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:111877600-111881200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:111877600-111881400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:111877800-111880800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:111877800-111881000	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr2:111877800-111881000	Active TSS	A549	lung
12	chr2:111877800-111881000	Active TSS	Hela-S3	cervix
13	chr2:111877800-111881200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr2:111877800-111881400	Active TSS	Ovary	ovary
15	chr2:111877800-111881400	Active TSS	HSMMtube	muscle
16	chr2:111878000-111880800	Active TSS	Primary T cells from cord blood	blood
17	chr2:111878000-111881000	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr2:111878000-111881000	Active TSS	Aorta	Aorta
19	chr2:111878000-111881000	Active TSS	Brain Anterior Caudate	brain
20	chr2:111878000-111881000	Active TSS	Brain Substantia Nigra	brain
21	chr2:111878000-111881000	Active TSS	Gastric	stomach
22	chr2:111878000-111881000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr2:111878000-111881200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:111878000-111881200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:111878000-111881200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:111878000-111881200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr2:111878000-111881200	Active TSS	Fetal Lung	lung
28	chr2:111878000-111881200	Active TSS	Left Ventricle	heart
29	chr2:111878000-111881200	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr2:111878000-111881400	Active TSS	Fetal Kidney	kidney
31	chr2:111878200-111880800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:111878200-111880800	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr2:111878200-111880800	Active TSS	Liver	Liver
34	chr2:111878200-111881000	Bivalent/Poised TSS	Fetal Brain Female	brain
35	chr2:111878200-111881200	Active TSS	NHDF-Ad	bronchial
36	chr2:111878600-111881200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:111878800-111881200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:111878800-111881400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr2:111879200-111881200	Active TSS	Right Atrium	heart
40	chr2:111879200-111881800	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr2:111879400-111881200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
42	chr2:111879400-111881200	Active TSS	Fetal Intestine Large	intestine
43	chr2:111879600-111881000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:111879600-111881200	Active TSS	H9 Cell Line	embryonic stem cell
45	chr2:111879600-111881200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:111879600-111881200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:111879600-111881200	Active TSS	Brain Angular Gyrus	brain
48	chr2:111879600-111881400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:111879800-111880800	Active TSS	Colon Smooth Muscle	Colon
50	chr2:111879800-111880800	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links