Variant report

Variant	rs9867214
Chromosome Location	chr3:118666307-118666308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118661298..118663595-chr3:118665722..118667353,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf30-1	chr3:118665896-118667071	ENSG00000239877.1
2	lnc-C3orf30-1	chr3:118665896-118667088	ENSG00000239877.2
3	lnc-C3orf30-1	chr3:118665896-118667088	NONHSAT091372
4	lnc-C3orf30-1	chr3:118665896-118667088	NR_046230

Variant related genes	Relation type
ENSG00000239877	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10212391	0.89[AFR][1000 genomes]
rs1158699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492855	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495725	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496820	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435655	1.00[CEU][hapmap]
rs16829165	0.83[YRI][hapmap];0.91[AFR][1000 genomes]
rs16829179	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160054	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573387	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28592657	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821882	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41523948	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs4611809	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56728928	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58284747	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773865	1.00[CEU][hapmap]
rs6779428	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785161	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs6795523	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs6807110	1.00[CEU][hapmap]
rs6807838	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72966889	0.95[AFR][1000 genomes]
rs72968605	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629089	0.92[AFR][1000 genomes]
rs7633584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644623	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9817943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821022	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821458	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833229	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834188	0.84[AFR][1000 genomes]
rs9836642	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837571	0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs9854240	0.89[AFR][1000 genomes]
rs9855713	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860140	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861721	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs9873807	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874337	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118658000-118668400	Weak transcription	A549	lung
2	chr3:118661600-118666600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:118661800-118667000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:118662000-118666600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:118662000-118666800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:118662000-118666800	Weak transcription	Fetal Lung	lung
7	chr3:118662000-118667000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:118662000-118667200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:118662000-118668000	Enhancers	Primary T cells from cord blood	blood
10	chr3:118662000-118679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:118662000-118679800	Weak transcription	Ovary	ovary
12	chr3:118662200-118666800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:118662800-118666400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:118662800-118666600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:118662800-118666600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:118662800-118672000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:118662800-118672400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:118664400-118666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:118664400-118676400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:118664600-118666800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:118664600-118667200	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:118664800-118667400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:118665400-118668200	Weak transcription	Fetal Heart	heart
24	chr3:118665600-118667000	Weak transcription	K562	blood
25	chr3:118665600-118668000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:118665600-118668800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:118665600-118669000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:118666000-118667200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:118666200-118667000	Enhancers	Brain Substantia Nigra	brain
30	chr3:118666200-118668200	Weak transcription	Brain Anterior Caudate	brain
31	chr3:118666200-118677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links