Variant report

Variant	rs2054166
Chromosome Location	chr15:51974910-51974911
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51974418..51976599-chr15:51979066..51980619,2	K562	blood:
2	chr15:51974117..51976857-chr15:51978812..51980643,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10851502	0.88[YRI][hapmap]
rs11070859	0.83[YRI][hapmap]
rs11070863	0.89[ASN][1000 genomes]
rs11631725	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11634180	0.84[YRI][hapmap]
rs11634955	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11638106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11638154	0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12440990	0.89[YRI][hapmap]
rs1456299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1456300	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2124592	0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs2124875	0.89[YRI][hapmap]
rs2168474	0.91[ASN][1000 genomes]
rs2305716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2607119	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622775	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2652594	0.94[JPT][hapmap]
rs28576876	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899477	0.85[AMR][1000 genomes]
rs4774597	0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs4774598	0.80[AMR][1000 genomes]
rs4775968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs55982453	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60060794	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493505	0.83[YRI][hapmap]
rs7167760	0.94[CHB][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes]
rs7168749	0.87[ASN][1000 genomes]
rs7170217	0.86[YRI][hapmap]
rs7170444	0.84[YRI][hapmap]
rs7170980	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7171884	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7174495	0.89[YRI][hapmap]
rs7183479	0.94[CHB][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs744039	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8023455	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030121	0.81[AMR][1000 genomes]
rs8031875	0.80[AMR][1000 genomes]
rs8033234	0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8034197	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8037340	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9744054	0.84[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	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2054166	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51973000-51975000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:51973000-51975000	Active TSS	Fetal Brain Female	brain
3	chr15:51973000-51975400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr15:51973400-51975400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:51973600-51975200	Active TSS	Brain Angular Gyrus	brain
6	chr15:51974000-51975200	Active TSS	Brain Germinal Matrix	brain
7	chr15:51974200-51977200	Weak transcription	Brain Substantia Nigra	brain
8	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:51974400-51975000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:51974400-51983400	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:51974400-51990800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:51974400-52005200	Weak transcription	Brain Anterior Caudate	brain
13	chr15:51974600-51975000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:51974600-51975200	Weak transcription	Fetal Brain Male	brain
15	chr15:51974600-51983000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:51974600-51983200	Weak transcription	K562	blood
17	chr15:51974600-51984200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:51974600-51991000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:51974800-51975000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:51974800-51975000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:51974800-51975200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr15:51974800-51984600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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