Variant report

Variant	rs4854244
Chromosome Location	chr2:95737679-95737680
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	chr2:95724354..95726435-chr2:95734944..95737851,2	MCF-7	breast:
2	chr2:95724511..95727645-chr2:95737663..95740205,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs17119148	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1875402	0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1966272	0.81[EUR][1000 genomes]
rs2001254	0.85[EUR][1000 genomes]
rs2098768	0.81[EUR][1000 genomes]
rs2291991	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2320619	0.95[EUR][1000 genomes]
rs2320620	0.95[CEU][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2320621	0.84[EUR][1000 genomes]
rs2320624	0.84[EUR][1000 genomes]
rs3105100	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3105101	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3105102	0.83[EUR][1000 genomes]
rs3105104	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs3105105	0.90[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs3112221	0.86[EUR][1000 genomes]
rs3112222	0.85[EUR][1000 genomes]
rs3112223	0.86[EUR][1000 genomes]
rs3112225	0.95[CEU][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes]
rs3112228	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs3112229	0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs3112230	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs3112231	0.89[EUR][1000 genomes]
rs3112982	0.90[CEU][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112983	0.90[CEU][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3112984	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3112985	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3112986	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3112987	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112988	0.86[ASN][1000 genomes]
rs3112990	0.86[ASN][1000 genomes]
rs3112995	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs3112996	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3112997	0.95[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3112999	0.80[EUR][1000 genomes]
rs3113000	0.84[EUR][1000 genomes]
rs3113001	0.84[EUR][1000 genomes]
rs4241315	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs4854241	0.84[GIH][hapmap]
rs4854243	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4854247	0.83[EUR][1000 genomes]
rs6719098	0.83[EUR][1000 genomes]
rs6723333	0.91[EUR][1000 genomes]
rs6725821	0.95[CEU][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7565772	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs7582368	0.89[CEU][hapmap];0.87[GIH][hapmap]
rs7585473	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs872580	0.89[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv3390169	chr2:95735525-95737948	Enhancers Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4854244	ZNF514	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95729800-95737800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:95729800-95740600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:95732200-95742400	Weak transcription	Pancreas	Pancrea
4	chr2:95733400-95742400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:95734200-95742400	Weak transcription	Right Atrium	heart
6	chr2:95737200-95741400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr2:95737200-95742400	Enhancers	Brain Angular Gyrus	brain
8	chr2:95737200-95742400	Enhancers	Brain Anterior Caudate	brain
9	chr2:95737200-95742400	Enhancers	Brain Hippocampus Middle	brain
10	chr2:95737400-95737800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:95737400-95740000	Enhancers	Thymus	Thymus
12	chr2:95737400-95740200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:95737400-95742400	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:95737400-95742400	Enhancers	Brain Substantia Nigra	brain
15	chr2:95737600-95737800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:95737600-95737800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:95737600-95738000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:95737600-95739800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:95737600-95740000	Enhancers	Fetal Thymus	thymus

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