Variant report

Variant	rs10189330
Chromosome Location	chr2:99389870-99389871
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:99384652-99389971	K562	blood:	n/a	n/a
2	RUNX3	chr2:99389630-99390054	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:99389829-99389879	HMEC	breast:	n/a
2	chr2:99389829-99389879	MCF-7	breast:	n/a
3	chr2:99389829-99389879	PrEC	prostate:	n/a
4	chr2:99389829-99389879	ProgFib	skin:	n/a
5	chr2:99389829-99389879	Jurkat	blood:	n/a
6	chr2:99389829-99389879	H1-hESC	embryonic stem cell:	embryo
7	chr2:99389829-99389879	GM12891	blood:	n/a
8	chr2:99389829-99389879	NHBE	bronchial:	n/a
9	chr2:99389829-99389879	HepG2	liver:	n/a
10	chr2:99389829-99389879	ECC-1	luminal epithelium:	n/a
11	chr2:99389829-99389879	SK-N-MC	brain:	n/a
12	chr2:99389829-99389879	HCF	heart:	n/a
13	chr2:99389829-99389879	HIPEpiC	eye:	n/a
14	chr2:99389829-99389879	AG10803	skin:	n/a
15	chr2:99389829-99389879	SKMC	muscle:	n/a
16	chr2:99389829-99389879	AG09309	skin:	n/a
17	chr2:99389829-99389879	NB4	blood:	n/a
18	chr2:99389829-99389879	BJ	skin:	n/a
19	chr2:99389829-99389879	HRCEpiC	kidney:	n/a
20	chr2:99389829-99389879	HEEpiC	esophagus:	n/a
21	chr2:99389829-99389879	RPTEC	kidney:	n/a
22	chr2:99389829-99389879	HCM	heart:	n/a
23	chr2:99389829-99389879	T-47D	breast:	n/a
24	chr2:99389829-99389879	NH-A	brain:	n/a
25	chr2:99389829-99389879	GM12892	blood:	n/a
26	chr2:99389829-99389879	NHDF-neo	bronchial:	n/a
27	chr2:99389829-99389879	HRE	kidney:	n/a
28	chr2:99389829-99389879	U87	brain:	n/a
29	chr2:99389829-99389879	ovcar-3	ovarian:	n/a
30	chr2:99389829-99389879	GM19239	blood:	n/a
31	chr2:99389829-99389879	GM12878	blood:	n/a
32	chr2:99389829-99389879	Hela-S3	cervix:	n/a
33	chr2:99389829-99389879	Caco-2	colon:	n/a
34	chr2:99389829-99389879	HNPCEpiC	eye:	n/a
35	chr2:99389829-99389879	SK-N-SH_RA	brain:	n/a
36	chr2:99389829-99389879	AG04450	lung:	fetal
37	chr2:99389829-99389879	HRPEpiC	eye:	n/a
38	chr2:99389829-99389879	PFSK-1	brain:	n/a
39	chr2:99389829-99389879	NT2-D1	testis:	n/a
40	chr2:99389829-99389879	Hepatocyte	liver:	n/a
41	chr2:99389829-99389879	HAEpiC	amniotic membrane:	n/a
42	chr2:99389829-99389879	LNCaP	prostate:	n/a
43	chr2:99389829-99389879	HCPEpiC	choroid plexus:	n/a
44	chr2:99389829-99389879	SAEC	small airway:	n/a
45	chr2:99389829-99389879	AG04449	skin:	fetal
46	chr2:99389829-99389879	A549	lung:	n/a
47	chr2:99389829-99389879	K562	blood:	n/a
48	chr2:99389829-99389879	HL-60	blood:	n/a
49	chr2:99389829-99389879	PANC-1	pancreas:	n/a
50	chr2:99389829-99389879	AG09319	gingival:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:
2	chr2:99384290..99389208-chr2:99389339..99394045,5	MCF-7	breast:
3	chr2:99389818..99391649-chr2:99395102..99396877,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226791	TF binding region
ENSG00000226791	CpG island
ENSG00000071073	Chromatin interaction
ENSG00000226791	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10166044	0.81[ASN][1000 genomes]
rs12615689	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs12999225	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13389386	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1356424	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2276604	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6712597	0.83[ASN][1000 genomes]
rs6716514	0.83[ASN][1000 genomes]
rs6757099	0.81[ASN][1000 genomes]
rs7557295	0.85[ASN][1000 genomes]
rs7570815	0.85[ASN][1000 genomes]
rs7578035	0.89[EUR][1000 genomes]
rs7581128	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581349	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs7582382	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9308815	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99385800-99394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
3	chr2:99386200-99391600	Weak transcription	Fetal Brain Female	brain
4	chr2:99386600-99391000	Weak transcription	Fetal Brain Male	brain
5	chr2:99386800-99391400	Weak transcription	Esophagus	oesophagus
6	chr2:99387600-99392000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:99387800-99390200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:99388000-99391400	Weak transcription	Pancreas	Pancrea
9	chr2:99388600-99392200	Weak transcription	Lung	lung
10	chr2:99389000-99390200	Enhancers	GM12878-XiMat	blood
11	chr2:99389000-99390400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr2:99389000-99390600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:99389000-99391800	Weak transcription	HepG2	liver
14	chr2:99389000-99392400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:99389000-99393000	Enhancers	Fetal Thymus	thymus
16	chr2:99389000-99393800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:99389200-99390000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr2:99389200-99390600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:99389200-99391200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:99389200-99391600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:99389200-99392000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:99389200-99392000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:99389200-99392400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr2:99389200-99392600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:99389400-99391600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:99389400-99391600	Enhancers	Primary T cells from cord blood	blood
27	chr2:99389400-99391600	Weak transcription	HMEC	breast
28	chr2:99389400-99391800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:99389400-99391800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:99389400-99392600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:99389400-99392800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr2:99389600-99391400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:99389600-99392000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:99389600-99392200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:99389800-99390000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:99389800-99390600	Weak transcription	Thymus	Thymus
37	chr2:99389800-99390600	Enhancers	Dnd41	blood
38	chr2:99389800-99391200	Enhancers	H1 Cell Line	embryonic stem cell

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