Variant report

Variant	rs889854
Chromosome Location	chr2:95959812-95959813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:95959772-95959953	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:95958593-95959958	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:95959572-95959894	ProgFib	skin:	n/a	n/a
4	POLR2A	chr2:95959655-95959882	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:95941675..95944170-chr2:95957167..95960145,2	MCF-7	breast:
2	chr2:95957914..95959837-chr2:95961824..95963921,3	K562	blood:
3	chr2:95924662..95927422-chr2:95957580..95961049,3	MCF-7	breast:
4	chr2:95933873..95936571-chr2:95958114..95960350,2	MCF-7	breast:

Variant related genes	Relation type
KCNIP3	TF binding region
ENSG00000115041	Chromatin interaction
ENSG00000155066	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2113418	0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.88[ASN][1000 genomes]
rs2278067	0.87[GIH][hapmap]
rs2320433	0.84[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap]
rs3112992	0.89[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[YRI][hapmap]
rs3112998	0.89[ASW][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs3821340	0.81[GIH][hapmap]
rs6719142	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7563891	0.80[ASN][1000 genomes]
rs869186	0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1007627	chr2:95878031-95973743	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv535822	chr2:95878031-95973743	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised 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
7	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1003196	chr2:95935031-95988314	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv482871	chr2:95936531-96036880	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1010345	chr2:95939355-95988314	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv999838	chr2:95945923-96003473	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs889854	ZNF514	cis	parietal	SCAN
rs889854	ZNF514	cis	cerebellum	SCAN
rs889854	ATP4B	trans	parietal	SCAN
rs889854	ZNF514	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95931400-95961000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:95931400-95961600	Weak transcription	Brain Substantia Nigra	brain
3	chr2:95932400-95961600	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:95946800-95960000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:95947800-95960800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:95954400-95962600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:95955400-95961200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:95956400-95961400	Weak transcription	Stomach Mucosa	stomach
9	chr2:95956400-95962200	Weak transcription	Gastric	stomach
10	chr2:95956400-95965800	Weak transcription	Esophagus	oesophagus
11	chr2:95957800-95962200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:95958200-95961400	Weak transcription	Colonic Mucosa	Colon
13	chr2:95958200-95963000	Enhancers	Pancreas	Pancrea
14	chr2:95958400-95961000	Weak transcription	Fetal Brain Female	brain
15	chr2:95959000-95960800	Weak transcription	Brain Anterior Caudate	brain
16	chr2:95959000-95960800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:95959200-95960400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:95959200-95962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:95959600-95960800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:95959600-95962800	Weak transcription	Right Atrium	heart
21	chr2:95959800-95960000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links