Variant report

Variant	rs4851279
Chromosome Location	chr2:100879797-100879798
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100879064..100881407-chr2:100995755..100997926,2	MCF-7	breast:
2	chr2:100879379..100882180-chr2:100906907..100909582,4	MCF-7	breast:
3	chr2:100877002..100888885-chr2:100934823..100940762,23	MCF-7	breast:
4	chr2:100879191..100881386-chr2:100993476..100996213,2	MCF-7	breast:
5	chr2:100879014..100880290-chr2:100996973..100998375,14	MCF-7	breast:
6	chr2:100878643..100880888-chr2:100907492..100909514,2	K562	blood:
7	chr2:100878848..100880953-chr2:101033016..101035489,3	K562	blood:
8	chr2:100879538..100882324-chr2:100997148..100999521,3	K562	blood:
9	chr2:100879002..100880063-chr2:100997058..100998343,16	K562	blood:
10	chr2:100879370..100880923-chr2:100934269..100935814,2	MCF-7	breast:
11	chr2:100879047..100879970-chr2:100997375..100998193,6	MCF-7	breast:
12	chr2:100879489..100880003-chr2:101038489..101039474,2	K562	blood:
13	chr2:100877863..100879986-chr2:100936694..100939073,4	MCF-7	breast:
14	chr2:100876613..100880348-chr2:101031611..101035939,8	K562	blood:
15	chr2:100878525..100880685-chr2:100881157..100883249,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115526	Chromatin interaction
ENSG00000270699	Chromatin interaction
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10174820	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs10176062	0.82[JPT][hapmap]
rs10195018	0.81[JPT][hapmap]
rs11890655	0.82[JPT][hapmap]
rs11902303	0.82[JPT][hapmap]
rs12615454	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13391517	0.82[JPT][hapmap]
rs13409545	0.82[JPT][hapmap]
rs17023901	0.81[JPT][hapmap]
rs2871340	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs34529583	0.89[ASN][1000 genomes]
rs3748928	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4322861	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4438499	0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4455176	0.89[ASN][1000 genomes]
rs4850925	0.82[JPT][hapmap]
rs4851278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542925	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6723909	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7556910	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4851279	ITPRIPL1	cis	cerebellum	SCAN
rs4851279	C2orf29	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100864200-100879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100865800-100879800	Weak transcription	Right Atrium	heart
3	chr2:100874600-100891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:100875200-100881600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:100877600-100879800	Weak transcription	Fetal Brain Male	brain
6	chr2:100877600-100888600	Weak transcription	Ovary	ovary
7	chr2:100877800-100880400	Weak transcription	Placenta	Placenta
8	chr2:100879000-100887000	Weak transcription	Gastric	stomach
9	chr2:100879200-100880200	Enhancers	Hela-S3	cervix
10	chr2:100879200-100880600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:100879400-100880000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:100879400-100880600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:100879400-100880600	Weak transcription	Fetal Lung	lung
14	chr2:100879400-100880800	Enhancers	K562	blood
15	chr2:100879400-100883200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:100879400-100891200	Weak transcription	Brain Anterior Caudate	brain
17	chr2:100879400-100896200	Weak transcription	Spleen	Spleen
18	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
19	chr2:100879600-100880400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr2:100879600-100881000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:100879600-100881000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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