Variant report

Variant	rs1681817
Chromosome Location	chr3:136473728-136473729
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: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	chr3:136466613..136474326-chr3:136579481..136583133,10	K562	blood:
2	chr3:136309415..136311669-chr3:136473283..136476207,2	K562	blood:
3	chr3:136472151..136474742-chr3:136749777..136751390,2	K562	blood:
4	chr3:136468701..136475672-chr3:136535815..136540749,9	K562	blood:
5	chr3:136472622..136474527-chr3:136477300..136478827,2	K562	blood:
6	chr3:136469311..136474326-chr3:136579207..136583133,7	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM22-1	chr3:136471472-136474622	ENSG00000261758.1

No data

Variant related genes	Relation type
ENSG00000168917	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000158092	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513014	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10935186	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11919030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12107125	0.92[ASN][1000 genomes]
rs12486911	1.00[YRI][hapmap]
rs1280622	0.88[EUR][1000 genomes]
rs1280624	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1729951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2062322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs28489907	0.90[ASN][1000 genomes]
rs34992220	0.92[JPT][hapmap]
rs35874192	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4038587	0.92[CEU][hapmap]
rs4408829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4521165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6439649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6439655	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6764567	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6789329	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6791142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6802702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs7616204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7618871	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7637129	0.82[EUR][1000 genomes]
rs900818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940174	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9813596	0.84[ASN][1000 genomes]
rs9821478	0.93[JPT][hapmap]
rs9825700	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9833207	0.92[JPT][hapmap]
rs9836231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.84[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	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1681817	PCCB	cis	multi-tissue	Pritchard
rs1681817	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136472200-136474200	Weak transcription	Esophagus	oesophagus
2	chr3:136473000-136474000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:136473000-136474000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:136473000-136474000	Weak transcription	Hela-S3	cervix
5	chr3:136473000-136474200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:136473000-136474200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:136473000-136474400	Enhancers	GM12878-XiMat	blood
8	chr3:136473000-136476600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:136473000-136476800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:136473000-136476800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:136473000-136477200	Weak transcription	Adipose Nuclei	Adipose
12	chr3:136473200-136474200	Weak transcription	Left Ventricle	heart
13	chr3:136473200-136474200	Weak transcription	Pancreas	Pancrea
14	chr3:136473200-136476600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:136473200-136476800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:136473200-136477200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:136473400-136475600	Weak transcription	NHEK	skin
18	chr3:136473600-136474200	Enhancers	K562	blood
19	chr3:136473600-136476400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:136473600-136476800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:136473600-136477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:136473600-136477000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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