Variant report

Variant	rs2414117
Chromosome Location	chr15:52032023-52032024
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:52031979-52032145	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52029378..52032499-chr15:52121077..52123299,3	MCF-7	breast:
2	chr15:52029591..52032408-chr15:52042418..52044684,3	K562	blood:
3	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
4	chr15:51913765..51915437-chr15:52031923..52034915,2	MCF-7	breast:
5	chr15:52030420..52032691-chr15:52120807..52123246,2	MCF-7	breast:
6	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

No data

Variant related genes	Relation type
LYSMD2	TF binding region
ENSG00000140280	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000259377	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10444798	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10444823	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10775145	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070864	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070865	0.81[AMR][1000 genomes]
rs11630084	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11632106	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11636345	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11638161	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638766	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11638820	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12903707	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12905283	0.91[AMR][1000 genomes]
rs12917133	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1350174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466276	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545602	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1867984	0.80[EUR][1000 genomes]
rs1902430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972689	0.84[EUR][1000 genomes]
rs2006772	0.83[EUR][1000 genomes]
rs2014638	0.84[EUR][1000 genomes]
rs2034857	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2034858	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2077743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168475	0.84[ASN][1000 genomes]
rs2264339	0.85[EUR][1000 genomes]
rs2414116	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2414119	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2436661	0.83[EUR][1000 genomes]
rs2554305	0.85[EUR][1000 genomes]
rs2554306	0.85[EUR][1000 genomes]
rs2554307	0.85[EUR][1000 genomes]
rs2554308	0.85[EUR][1000 genomes]
rs2554334	0.80[EUR][1000 genomes]
rs2554345	0.80[EUR][1000 genomes]
rs2570224	0.80[EUR][1000 genomes]
rs2570231	0.83[EUR][1000 genomes]
rs2570233	0.84[EUR][1000 genomes]
rs2570235	0.84[EUR][1000 genomes]
rs2570236	0.83[EUR][1000 genomes]
rs2570237	0.82[EUR][1000 genomes]
rs2570251	0.83[EUR][1000 genomes]
rs2570252	0.80[EUR][1000 genomes]
rs2570253	0.80[EUR][1000 genomes]
rs2623254	0.85[EUR][1000 genomes]
rs2623259	0.80[EUR][1000 genomes]
rs2623262	0.80[EUR][1000 genomes]
rs3088312	0.82[AMR][1000 genomes]
rs3751596	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794530	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3794534	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3794535	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3794536	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4238383	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4502160	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4534783	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4622456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774602	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775978	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775982	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4775983	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs526556	0.83[ASN][1000 genomes]
rs55843525	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55887408	0.86[EUR][1000 genomes]
rs6493515	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493518	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6493519	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6493522	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493523	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689884	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7163176	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165585	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166110	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7166962	0.85[AMR][1000 genomes]
rs7168659	0.85[AMR][1000 genomes]
rs7171459	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173375	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174941	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7181553	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7182917	0.83[EUR][1000 genomes]
rs8024081	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8024088	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8024589	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8026521	0.91[AMR][1000 genomes]
rs8027721	0.85[AMR][1000 genomes]
rs8028258	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028890	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8041268	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2414117	LYSMD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52030600-52032600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr15:52030600-52032800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:52030600-52043200	Weak transcription	Gastric	stomach
4	chr15:52030800-52032400	Enhancers	K562	blood
5	chr15:52030800-52032600	Enhancers	Primary T cells from cord blood	blood
6	chr15:52030800-52032800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr15:52031000-52032400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:52031000-52032600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:52031000-52033400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:52031200-52043000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:52031400-52032400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:52031600-52032400	Enhancers	Fetal Thymus	thymus
13	chr15:52031800-52032400	Enhancers	Thymus	Thymus
14	chr15:52032000-52032600	Enhancers	Primary T cells fromperipheralblood	blood

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