Variant report

Variant	rs2138349
Chromosome Location	chr2:172543397-172543398
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	CTCF	chr2:172543260-172543410	GM12872	blood:	n/a	n/a
2	CEBPZ	chr2:172543343-172543421	HepG2	liver:	n/a	n/a
3	SIX5	chr2:172543331-172544660	A549	lung:	n/a	chr2:172543877-172543891 chr2:172543914-172543923 chr2:172543879-172543888 chr2:172543881-172543890
4	IRF1	chr2:172543105-172543425	K562	blood:	n/a	chr2:172543384-172543397
5	HCFC1	chr2:172543385-172544891	Hela-S3	cervix:	n/a	n/a
6	JUN	chr2:172543176-172545750	K562	blood:	n/a	chr2:172544518-172544528 chr2:172544518-172544527 chr2:172544518-172544528 chr2:172544517-172544529 chr2:172544518-172544528 chr2:172544518-172544528
7	EP300	chr2:172543244-172545036	K562	blood:	n/a	chr2:172543389-172543399 chr2:172544264-172544274 chr2:172544519-172544528

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172542927..172544505-chr2:172566367..172569318,2	K562	blood:
2	chr2:172508719..172510692-chr2:172541711..172543434,2	MCF-7	breast:

Variant related genes	Relation type
DYNC1I2	TF binding region
ENSG00000077380	Chromatin interaction
ENSG00000268821	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11673831	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11675404	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11675891	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12991441	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13016580	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13017695	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13021138	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13024662	0.85[AMR][1000 genomes]
rs1554259	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17427311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17427473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17499306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17499502	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17848721	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1996424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2357062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34108287	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34221876	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34632749	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34962243	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35162284	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3770459	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62182397	0.84[AFR][1000 genomes]
rs62184174	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72889853	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74173119	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs979955	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2138349	KLHL23	cis	cerebellum	SCAN
rs2138349	MAP1D	cis	parietal	SCAN
rs2138349	B3GALT1	cis	cerebellum	SCAN
rs2138349	SLC25A12	cis	parietal	SCAN
rs2138349	SLC25A12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172539400-172543600	Weak transcription	K562	blood

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