Variant report

Variant	rs2138484
Chromosome Location	chr2:183977942-183977943
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	GATA1	chr2:183977180-183978022	PBDE	blood:	n/a	n/a
2	EP300	chr2:183977379-183978770	K562	blood:	n/a	chr2:183978740-183978754
3	KAP1	chr2:183977385-183977956	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:183901632..183905004-chr2:183977592..183981292,4	K562	blood:
2	chr2:183967945..183970518-chr2:183975860..183978004,2	K562	blood:
3	chr2:183977930..183980927-chr2:183984054..183985620,2	MCF-7	breast:
4	chr2:183976023..183978343-chr2:183982634..183984997,2	K562	blood:

Variant related genes	Relation type
ENSG00000224643	TF binding region
NUP35	TF binding region
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10153562	1.00[YRI][hapmap]
rs10165922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10170163	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10174477	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10179245	0.82[YRI][hapmap]
rs10181735	0.82[YRI][hapmap]
rs10183561	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10191080	0.81[YRI][hapmap]
rs10200193	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201194	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10460315	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931061	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11692613	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12463411	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12693331	0.89[ASN][1000 genomes]
rs13399265	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13419900	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1400131	0.84[MEX][hapmap]
rs1473617	0.81[YRI][hapmap]
rs16823717	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16823721	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16823967	1.00[CHB][hapmap]
rs16823970	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16823971	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16823974	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16823976	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16824001	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1882440	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882444	0.84[MEX][hapmap]
rs2138482	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2138485	0.91[ASN][1000 genomes]
rs2176228	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2247840	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2368335	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2368354	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2675045	0.84[MEX][hapmap]
rs2675117	1.00[CHB][hapmap]
rs2705714	0.91[ASN][1000 genomes]
rs2944346	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3748879	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4597478	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4666607	1.00[CHB][hapmap]
rs4666885	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4666887	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666888	0.82[YRI][hapmap]
rs55942934	0.84[ASN][1000 genomes]
rs56271556	0.84[ASN][1000 genomes]
rs59041013	0.84[ASN][1000 genomes]
rs61283216	0.84[ASN][1000 genomes]
rs61526412	0.84[ASN][1000 genomes]
rs6742203	0.89[ASN][1000 genomes]
rs73035651	0.82[ASN][1000 genomes]
rs73036601	0.84[ASN][1000 genomes]
rs7569854	0.82[YRI][hapmap]
rs7601585	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7607102	0.82[YRI][hapmap]
rs7608545	0.82[YRI][hapmap]
rs867340	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs925805	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs925806	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv2763287	chr2:183939173-184037893	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3356302	chr2:183962495-183989877	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2138484	NUP35	cis	cerebellum	SCAN
rs2138484	NCKAP1	cis	cerebellum	SCAN
rs2138484	DUSP19	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183954600-183988400	Weak transcription	Aorta	Aorta
2	chr2:183977200-183978200	Flanking Active TSS	K562	blood

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