Variant report

Variant	rs7289250
Chromosome Location	chr22:30234218-30234219
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:270)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:270 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr22:30233831-30234581	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:30233945-30234739	MCF-7	breast:	n/a	n/a
3	MAX	chr22:30233859-30234627	Hela-S3	cervix:	n/a	chr22:30233934-30233943
4	RFX5	chr22:30233969-30234660	Hela-S3	cervix:	n/a	n/a
5	ETS1	chr22:30233995-30234459	K562	blood:	n/a	chr22:30234282-30234296 chr22:30234301-30234312 chr22:30234282-30234291
6	CHD2	chr22:30233825-30234564	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr22:30233692-30234551	Hela-S3	cervix:	n/a	n/a
8	MAX	chr22:30233789-30234682	ECC-1	luminal epithelium:	n/a	chr22:30233934-30233943
9	POLR2A	chr22:30233948-30234858	GM12878	blood:	n/a	n/a
10	YY1	chr22:30233833-30234554	K562	blood:	n/a	chr22:30234301-30234310
11	E2F6	chr22:30234141-30234356	K562	blood:	n/a	chr22:30234296-30234306 chr22:30234301-30234310
12	ELF1	chr22:30233793-30234768	MCF-7	breast:	n/a	chr22:30234278-30234291 chr22:30234245-30234258
13	NR2F2	chr22:30233959-30234662	K562	blood:	n/a	n/a
14	TAF1	chr22:30234017-30234544	H1-neurons	neurons:	n/a	n/a
15	USF1	chr22:30234203-30234711	ECC-1	luminal epithelium:	n/a	n/a
16	CHD2	chr22:30233977-30234614	K562	blood:	n/a	n/a
17	ATF2	chr22:30234033-30234573	GM12878	blood:	n/a	n/a
18	POLR2A	chr22:30233855-30234827	HUVEC	blood vessel:	n/a	n/a
19	HEY1	chr22:30233982-30234739	HepG2	liver:	n/a	n/a
20	E2F4	chr22:30234163-30234701	MCF10A-Er-Src	breast:	n/a	chr22:30234296-30234306 chr22:30234301-30234310
21	POLR2A	chr22:30233957-30234790	H1-hESC	embryonic stem cell:	n/a	n/a
22	JUND	chr22:30234168-30234687	K562	blood:	n/a	chr22:30234546-30234556
23	ELF1	chr22:30233873-30234643	GM12878	blood:	n/a	chr22:30234278-30234291 chr22:30234245-30234258
24	POLR2A	chr22:30233837-30234778	GM12892	blood:	n/a	n/a
25	TAF1	chr22:30234208-30234643	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr22:30234015-30234468	K562	blood:	n/a	n/a
27	CREB1	chr22:30234006-30234517	A549	lung:	n/a	n/a
28	POLR2A	chr22:30233958-30234631	HCT-116	colon:	n/a	n/a
29	ETS1	chr22:30234050-30234469	A549	lung:	n/a	chr22:30234282-30234296 chr22:30234301-30234312 chr22:30234282-30234291
30	SP4	chr22:30234166-30234654	H1-hESC	embryonic stem cell:	n/a	chr22:30234299-30234315 chr22:30234391-30234407 chr22:30234367-30234378 chr22:30234393-30234409 chr22:30234297-30234313 chr22:30234405-30234416
31	GABPA	chr22:30233852-30234617	MCF-7	breast:	n/a	chr22:30234301-30234310
32	MXI1	chr22:30234214-30234419	K562	blood:	n/a	n/a
33	POLR2A	chr22:30234165-30234564	K562	blood:	n/a	n/a
34	POLR2A	chr22:30233978-30234585	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr22:30233846-30234727	GM12891	blood:	n/a	n/a
36	POLR2A	chr22:30234047-30234309	A549	lung:	n/a	n/a
37	ELK1	chr22:30234143-30234345	K562	blood:	n/a	n/a
38	MAZ	chr22:30233907-30234608	HepG2	liver:	n/a	chr22:30233934-30233943
39	POLR2A	chr22:30233907-30234733	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr22:30233796-30234703	H1-neurons	neurons:	n/a	n/a
41	REST	chr22:30233464-30234918	H1-neurons	neurons:	n/a	chr22:30233992-30234005
42	GABPA	chr22:30233745-30234620	A549	lung:	n/a	chr22:30234301-30234310
43	CEBPB	chr22:30234169-30234639	Hela-S3	cervix:	n/a	n/a
44	GABPA	chr22:30233731-30234472	K562	blood:	n/a	chr22:30234301-30234310
45	POLR2A	chr22:30233997-30234723	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr22:30234088-30234289	A549	lung:	n/a	n/a
47	POLR2A	chr22:30233869-30234833	GM12892	blood:	n/a	n/a
48	TBP	chr22:30234037-30234654	K562	blood:	n/a	n/a
49	RCOR1	chr22:30234124-30234849	GM12878	blood:	n/a	n/a
50	ELF1	chr22:30233911-30234729	SK-N-SH	brain:	n/a	chr22:30234278-30234291 chr22:30234245-30234258

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:30234213-30234263	HL-60	blood:	n/a
2	chr22:30234213-30234263	U87	brain:	n/a
3	chr22:30234213-30234263	AG09309	skin:	n/a
4	chr22:30234213-30234263	HCM	heart:	n/a
5	chr22:30234213-30234263	K562	blood:	n/a
6	chr22:30234213-30234263	H1-hESC	embryonic stem cell:	embryo
7	chr22:30234213-30234263	Caco-2	colon:	n/a
8	chr22:30234213-30234263	NHBE	bronchial:	n/a
9	chr22:30234213-30234263	HNPCEpiC	eye:	n/a
10	chr22:30234213-30234263	LNCaP	prostate:	n/a
11	chr22:30234213-30234263	AG10803	skin:	n/a
12	chr22:30234213-30234263	IMR90	lung:	fetal
13	chr22:30234213-30234263	PrEC	prostate:	n/a
14	chr22:30234213-30234263	GM12892	blood:	n/a
15	chr22:30234213-30234263	PFSK-1	brain:	n/a
16	chr22:30234213-30234263	HRE	kidney:	n/a
17	chr22:30234213-30234263	SK-N-SH_RA	brain:	n/a
18	chr22:30234213-30234263	SAEC	small airway:	n/a
19	chr22:30234213-30234263	HPAEpiC	pulmonary alveolar:	n/a
20	chr22:30234213-30234263	T-47D	breast:	n/a
21	chr22:30234213-30234263	NH-A	brain:	n/a
22	chr22:30234213-30234263	MCF-7	breast:	n/a
23	chr22:30234213-30234263	AG09319	gingival:	n/a
24	chr22:30234213-30234263	ovcar-3	ovarian:	n/a
25	chr22:30234213-30234263	SK-N-SH	brain:	n/a
26	chr22:30234213-30234263	SKMC	muscle:	n/a
27	chr22:30234213-30234263	PANC-1	pancreas:	n/a
28	chr22:30234213-30234263	ECC-1	luminal epithelium:	n/a
29	chr22:30234213-30234263	GM12891	blood:	n/a
30	chr22:30234213-30234263	NB4	blood:	n/a
31	chr22:30234213-30234263	ProgFib	skin:	n/a
32	chr22:30234213-30234263	HAEpiC	amniotic membrane:	n/a
33	chr22:30234213-30234263	AoSMC	blood vessel:	n/a
34	chr22:30234213-30234263	HCPEpiC	choroid plexus:	n/a
35	chr22:30234213-30234263	HEK293	kidney:	embryo
36	chr22:30234213-30234263	AG04450	lung:	fetal
37	chr22:30234213-30234263	CMK	blood:	n/a
38	chr22:30234213-30234263	BE2_C	brain:	n/a
39	chr22:30234213-30234263	MCF10A-Er-Src	breast:	n/a
40	chr22:30234213-30234263	SK-N-MC	brain:	n/a
41	chr22:30234213-30234263	Jurkat	blood:	n/a
42	chr22:30234213-30234263	HRPEpiC	eye:	n/a
43	chr22:30234213-30234263	HMEC	breast:	n/a
44	chr22:30234213-30234263	Hela-S3	cervix:	n/a
45	chr22:30234213-30234263	HCF	heart:	n/a
46	chr22:30234213-30234263	RPTEC	kidney:	n/a
47	chr22:30234213-30234263	HRCEpiC	kidney:	n/a
48	chr22:30234213-30234263	NT2-D1	testis:	n/a
49	chr22:30234213-30234263	Hepatocyte	liver:	n/a
50	chr22:30234213-30234263	GM19239	blood:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:46723531..46724116-chr22:30233901..30234633,2	Hela-S3	cervix:
2	chr22:30232954..30235817-chr22:30277750..30279574,2	MCF-7	breast:
3	chr22:30225765..30230715-chr22:30232604..30236000,6	K562	blood:
4	chr22:30221897..30227952-chr22:30230604..30235599,8	MCF-7	breast:
5	chr22:30199503..30202747-chr22:30231620..30235442,3	MCF-7	breast:
6	chr22:30228546..30230856-chr22:30232707..30235317,4	MCF-7	breast:
7	chr22:30228718..30231367-chr22:30232651..30236541,5	K562	blood:
8	chr22:30224439..30228420-chr22:30233600..30235751,3	K562	blood:
9	chr22:30226725..30230027-chr22:30233173..30235923,3	MCF-7	breast:
10	chr22:30162371..30164035-chr22:30233277..30234908,2	MCF-7	breast:
11	chr22:30209515..30211458-chr22:30232926..30235230,2	K562	blood:

No data

Variant related genes	Relation type
ASCC2	TF binding region
ASCC2	CpG island
ENSG00000100325	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000184076	Chromatin interaction
ENSG00000100330	Chromatin interaction
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1071962	0.88[ASN][1000 genomes]
rs12158466	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12159277	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12627866	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12628028	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12628234	0.83[EUR][1000 genomes]
rs12628545	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs14115	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16987142	0.85[EUR][1000 genomes]
rs16988049	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17711461	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17711508	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2018808	0.87[EUR][1000 genomes]
rs2240364	0.82[EUR][1000 genomes]
rs2240365	0.85[EUR][1000 genomes]
rs2240366	0.85[EUR][1000 genomes]
rs249399	0.81[ASN][1000 genomes]
rs28730892	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57122143	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58015017	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59394320	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997519	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs5997520	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs5997524	0.87[EUR][1000 genomes]
rs6006247	0.87[EUR][1000 genomes]
rs6006249	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6006250	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6006262	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60805530	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61616383	0.85[EUR][1000 genomes]
rs7285660	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7285800	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7287777	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73392899	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73394814	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73394831	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73394838	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs737728	0.85[EUR][1000 genomes]
rs740116	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8138165	0.80[AFR][1000 genomes];0.83[EUR][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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30232000-30234600	Active TSS	GM12878-XiMat	blood
2	chr22:30233000-30234400	Active TSS	Muscle Satellite Cultured Cells	--
3	chr22:30233000-30234600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30233000-30234800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr22:30233000-30234800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr22:30233200-30234400	Active TSS	HSMM	muscle
7	chr22:30233200-30234600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr22:30233200-30234600	Active TSS	Stomach Mucosa	stomach
9	chr22:30233200-30234600	Active TSS	A549	lung
10	chr22:30233200-30234600	Active TSS	NHLF	lung
11	chr22:30233200-30234800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr22:30233400-30234400	Active TSS	Brain Germinal Matrix	brain
13	chr22:30233400-30234600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr22:30233400-30234600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr22:30233400-30234600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr22:30233400-30234600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr22:30233400-30234600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr22:30233400-30234600	Bivalent/Poised TSS	HepG2	liver
19	chr22:30233400-30234600	Active TSS	HSMMtube	muscle
20	chr22:30233400-30234600	Active TSS	NHDF-Ad	bronchial
21	chr22:30233400-30234800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr22:30233400-30234800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr22:30233400-30235000	Active TSS	Fetal Kidney	kidney
24	chr22:30233600-30234400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr22:30233600-30234400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
26	chr22:30233600-30234600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:30233600-30234600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:30233600-30234600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:30233600-30234600	Active TSS	Brain Hippocampus Middle	brain
30	chr22:30233600-30234600	Active TSS	Left Ventricle	heart
31	chr22:30233600-30234600	Active TSS	Lung	lung
32	chr22:30233600-30234600	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr22:30233600-30234800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr22:30233600-30234800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr22:30233600-30234800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr22:30233600-30234800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr22:30233600-30234800	Active TSS	Aorta	Aorta
38	chr22:30233600-30235000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr22:30233800-30234400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr22:30233800-30234400	Active TSS	Liver	Liver
41	chr22:30233800-30234400	Active TSS	Gastric	stomach
42	chr22:30233800-30234400	Active TSS	NHEK	skin
43	chr22:30233800-30234600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:30233800-30234600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr22:30233800-30234600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr22:30233800-30234600	Active TSS	Primary T cells from cord blood	blood
47	chr22:30233800-30234600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr22:30233800-30234600	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr22:30233800-30234600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr22:30233800-30234600	Active TSS	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links