Variant report

Variant	rs2515401
Chromosome Location	chr2:113820476-113820477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113820207..113823045-chr2:113825463..113827849,2	MCF-7	breast:
2	chr2:113815604..113817991-chr2:113819036..113821911,2	K562	blood:
3	chr2:113815048..113817991-chr2:113819572..113821911,4	K562	blood:

Variant related genes	Relation type
ENSG00000136695	Chromatin interaction
ENSG00000136697	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10165797	0.95[CHB][hapmap]
rs10187916	0.84[AMR][1000 genomes]
rs10206428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123158	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs12475161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030063	0.81[CHD][hapmap]
rs13407508	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs1374285	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1374286	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1446521	0.94[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1530548	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1530550	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1530551	1.00[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1530552	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1530553	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1800930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1813048	0.82[AMR][1000 genomes]
rs1867832	0.80[AMR][1000 genomes]
rs1867833	0.80[AMR][1000 genomes]
rs2100071	0.94[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs2251872	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2251876	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252007	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2305150	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs2441375	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2441376	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2472187	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2472188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515391	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2515392	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2515394	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2515395	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2515396	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2515397	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2515398	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2515399	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2515400	0.82[AMR][1000 genomes]
rs2515402	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515404	0.94[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs2862772	0.90[CHB][hapmap]
rs2862853	0.94[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs3180234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3180235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145013	0.88[GIH][hapmap]
rs4849142	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs4849146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849150	0.80[ASN][1000 genomes]
rs6542110	0.81[AMR][1000 genomes]
rs6710007	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs6728769	0.82[AMR][1000 genomes]
rs6733859	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6748448	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6758965	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs7570267	0.81[CEU][hapmap]
rs7599662	0.94[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs768627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921065	0.82[CHB][hapmap]
rs957201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9678578	0.94[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs990524	0.94[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2515401	IL36B	cis	Esophagus Mucosa	GTEx
rs2515401	IL1F9	cis	cerebellum	SCAN
rs2515401	TEPP	trans	parietal	SCAN
rs2515401	LOC654433	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113817000-113825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:113817400-113821600	Enhancers	Placenta	Placenta
3	chr2:113817600-113826200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:113820400-113820600	Enhancers	Placenta Amnion	Placenta Amnion

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