Variant report

Variant	rs2871340
Chromosome Location	chr2:100884117-100884118
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100877002..100888885-chr2:100934823..100940762,23	MCF-7	breast:
2	chr2:100880223..100882269-chr2:100883813..100885486,2	MCF-7	breast:
3	chr2:100882680..100885040-chr2:100936367..100939347,3	MCF-7	breast:
4	chr2:100882860..100889379-chr2:100906197..100910186,11	MCF-7	breast:
5	chr2:100881955..100884810-chr2:100886206..100888187,2	K562	blood:
6	chr2:100252857..100253710-chr2:100883998..100884797,3	MCF-7	breast:
7	chr2:100883299..100887347-chr2:100906337..100908618,4	MCF-7	breast:
8	chr2:100881738..100884952-chr2:100887555..100890244,3	MCF-7	breast:
9	chr2:100882939..100884943-chr2:101037829..101040208,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11123823	0.86[JPT][hapmap]
rs11694723	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs12615454	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs13019179	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2067783	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs34529583	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4322861	0.89[ASN][1000 genomes]
rs4331524	0.90[EUR][1000 genomes]
rs4438499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4455176	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4622752	0.88[CEU][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs4851278	0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4851279	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4851288	0.81[CEU][hapmap]
rs6542922	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6723909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764828	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2871340	LONRF2	cis	cerebellum	SCAN
rs2871340	AFF3	cis	parietal	SCAN
rs2871340	ZNF667	trans	cerebellum	SCAN
rs2871340	CHST10	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100874600-100891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:100877600-100888600	Weak transcription	Ovary	ovary
3	chr2:100879000-100887000	Weak transcription	Gastric	stomach
4	chr2:100879400-100891200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:100879400-100896200	Weak transcription	Spleen	Spleen
6	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:100880000-100891400	Weak transcription	Brain Germinal Matrix	brain
8	chr2:100880200-100898400	Weak transcription	A549	lung
9	chr2:100881000-100887400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:100881000-100887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:100881200-100884200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:100881800-100887200	Weak transcription	K562	blood
13	chr2:100882000-100886400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:100882000-100887400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:100883200-100885800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:100883800-100884600	Enhancers	Placenta	Placenta

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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