Variant report

Variant	rs7166110
Chromosome Location	chr15:52042832-52042833
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52041917-52044815	Raji	blood:	n/a	n/a
2	POLR2A	chr15:52042188-52043672	GM12891	blood:	n/a	n/a
3	RELA	chr15:52042201-52043746	GM12891	blood:	n/a	n/a
4	MXI1	chr15:52042784-52045538	SK-N-SH	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
2	chr15:51913469..51917109-chr15:52042794..52045514,3	MCF-7	breast:
3	chr15:52041956..52043686-chr15:52074164..52076601,2	MCF-7	breast:
4	chr15:52029591..52032408-chr15:52042418..52044684,3	K562	blood:
5	chr15:52016515..52018648-chr15:52040542..52043046,2	MCF-7	breast:
6	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
7	chr15:52033609..52037215-chr15:52040115..52042966,3	MCF-7	breast:
8	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

No data

Variant related genes	Relation type
TMOD2	TF binding region
ENSG00000259377	TF binding region
ENSG00000128872	Chromatin interaction
ENSG00000140280	Chromatin interaction
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10444798	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10444823	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775145	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070864	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070865	0.85[AMR][1000 genomes]
rs11630084	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632106	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11636345	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11638161	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11638766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438686	0.85[ASN][1000 genomes]
rs12903707	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12905283	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs12917133	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1350174	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1466276	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1545602	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17705732	0.85[ASN][1000 genomes]
rs1811326	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867984	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1895863	0.81[ASN][1000 genomes]
rs1902430	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1972689	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2006772	0.86[EUR][1000 genomes]
rs2014638	0.87[EUR][1000 genomes]
rs2034856	0.86[AFR][1000 genomes]
rs2034857	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2034858	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2077743	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2264339	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303443	0.82[EUR][1000 genomes]
rs2414116	0.86[AFR][1000 genomes]
rs2414117	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414119	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2436661	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470619	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2554305	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2554306	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2554307	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2554308	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2554315	0.89[ASN][1000 genomes]
rs2554332	0.82[EUR][1000 genomes]
rs2554334	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2554336	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2554345	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2570224	0.83[EUR][1000 genomes]
rs2570228	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2570231	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2570233	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2570235	0.87[EUR][1000 genomes]
rs2570236	0.85[EUR][1000 genomes]
rs2570237	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2570251	0.86[EUR][1000 genomes]
rs2570252	0.83[EUR][1000 genomes]
rs2570253	0.83[EUR][1000 genomes]
rs2570258	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2570260	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593191	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2623254	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2623259	0.83[EUR][1000 genomes]
rs2623262	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3088312	0.86[AMR][1000 genomes]
rs3751596	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794530	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794534	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794535	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794536	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4502160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4534783	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4622456	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4774602	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775978	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775982	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4775983	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55843525	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55887408	0.88[EUR][1000 genomes]
rs58758283	0.85[ASN][1000 genomes]
rs60329909	0.86[ASN][1000 genomes]
rs6493515	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6493518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493519	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493522	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493523	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67895020	0.82[EUR][1000 genomes]
rs689884	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689922	0.94[ASN][1000 genomes]
rs690287	0.92[ASN][1000 genomes]
rs690638	0.92[ASN][1000 genomes]
rs7163176	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7165585	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7166962	0.89[AMR][1000 genomes]
rs7168659	0.89[AMR][1000 genomes]
rs7171459	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7173375	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174941	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176421	0.82[ASN][1000 genomes]
rs7181553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182917	0.85[EUR][1000 genomes]
rs72732952	0.81[ASN][1000 genomes]
rs8024081	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024088	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024589	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026521	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs8027721	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8028258	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8028890	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041268	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs919059	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9635308	0.94[ASN][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
rs7166110	LYSMD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52030600-52043200	Weak transcription	Gastric	stomach
2	chr15:52031200-52043000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52042200-52043000	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:52042600-52043000	Enhancers	Brain Angular Gyrus	brain
5	chr15:52042600-52043000	Enhancers	Brain Cingulate Gyrus	brain
6	chr15:52042600-52043000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr15:52042600-52043000	Bivalent Enhancer	Stomach Mucosa	stomach
8	chr15:52042600-52043200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52042600-52043400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:52042600-52043600	Flanking Active TSS	GM12878-XiMat	blood
11	chr15:52042800-52043000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr15:52042800-52043000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:52042800-52043000	Enhancers	Brain Hippocampus Middle	brain
14	chr15:52042800-52043000	Enhancers	Colon Smooth Muscle	Colon
15	chr15:52042800-52043000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr15:52042800-52043200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr15:52042800-52043400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:52042800-52043400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr15:52042800-52043600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr15:52042800-52043600	Flanking Active TSS	K562	blood
21	chr15:52042800-52044600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr15:52042800-52044600	Active TSS	Brain Anterior Caudate	brain
23	chr15:52042800-52044800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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