Variant report

Variant	rs922903
Chromosome Location	chr2:48342373-48342374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48340519..48342551-chr2:48370795..48372930,3	K562	blood:
2	chr2:48338567..48340069-chr2:48340476..48342562,2	K562	blood:
3	chr2:48342001..48342697-chr2:48647600..48648543,2	K562	blood:
4	chr2:48341598..48344591-chr2:48542825..48544946,2	K562	blood:
5	chr2:48337553..48343006-chr2:48644200..48649231,9	MCF-7	breast:
6	chr2:48340321..48343318-chr2:48346650..48348964,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXN2-5	chr2:48340114-48344953	NONHSAT070614

No data

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10196696	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10199698	0.85[JPT][hapmap]
rs10865228	0.93[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11125165	0.89[ASN][1000 genomes]
rs11125166	0.81[ASN][1000 genomes]
rs1483213	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1483221	0.82[AMR][1000 genomes]
rs2056138	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2128719	0.83[ASN][1000 genomes]
rs2136456	0.96[ASN][1000 genomes]
rs2220075	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2348717	1.00[ASN][1000 genomes]
rs2348718	0.96[ASN][1000 genomes]
rs2882003	0.89[ASN][1000 genomes]
rs4146603	0.89[ASN][1000 genomes]
rs4952901	0.81[AMR][1000 genomes]
rs4952905	0.96[ASN][1000 genomes]
rs4953548	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953549	1.00[ASN][1000 genomes]
rs4953552	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4953553	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4953555	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4953556	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953557	0.89[ASN][1000 genomes]
rs58178746	0.89[ASN][1000 genomes]
rs58525908	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6545018	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545021	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545023	0.89[ASN][1000 genomes]
rs6712238	1.00[ASN][1000 genomes]
rs6717617	0.85[JPT][hapmap]
rs6718037	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720994	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6722407	1.00[ASN][1000 genomes]
rs6723952	1.00[ASN][1000 genomes]
rs6732149	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6749276	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7566525	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7570354	0.89[ASN][1000 genomes]
rs7584401	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7584493	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7589460	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605361	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7605366	0.90[ASN][1000 genomes]
rs7609124	1.00[ASN][1000 genomes]
rs922902	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs963134	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9677729	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs973894	0.89[ASN][1000 genomes]
rs990063	0.89[ASN][1000 genomes]
rs990549	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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 target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48339400-48342400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:48339400-48342400	Weak transcription	Spleen	Spleen
3	chr2:48339400-48343600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:48339400-48345000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:48339600-48342400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr2:48339600-48342400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:48339600-48342600	Enhancers	Hela-S3	cervix
8	chr2:48339600-48342800	Enhancers	Fetal Intestine Large	intestine
9	chr2:48339600-48342800	Enhancers	Fetal Intestine Small	intestine
10	chr2:48339600-48342800	Enhancers	Placenta	Placenta
11	chr2:48339600-48344600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:48340000-48342400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:48340200-48342400	Enhancers	K562	blood
14	chr2:48340200-48342600	Enhancers	HMEC	breast
15	chr2:48340600-48342600	Enhancers	GM12878-XiMat	blood
16	chr2:48340800-48342400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:48340800-48347800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:48341000-48342400	Enhancers	HepG2	liver
19	chr2:48341000-48344400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:48341000-48345800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:48341200-48346600	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:48341600-48342600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:48341800-48342400	Enhancers	Adipose Nuclei	Adipose
24	chr2:48342000-48342400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:48342000-48342400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:48342000-48342600	Enhancers	Right Atrium	heart
27	chr2:48342000-48342600	Enhancers	Small Intestine	intestine
28	chr2:48342200-48342400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:48342200-48348200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:48342200-48353000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links