Variant report

Variant	rs11638154
Chromosome Location	chr15:51969416-51969417
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	GATA3	chr15:51969258-51969824	MCF-7	breast:	n/a	n/a
2	STAT3	chr15:51969281-51969529	MCF10A-Er-Src	breast:	n/a	chr15:51969377-51969385
3	STAT3	chr15:51969296-51969500	MCF10A-Er-Src	breast:	n/a	chr15:51969377-51969385

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51968757..51971365-chr15:51975638..51977391,2	MCF-7	breast:
2	chr15:51969219..51969771-chr17:58041529..58042444,2	MCF-7	breast:

Variant related genes	Relation type
SCG3	TF binding region
ENSG00000267302	Chromatin interaction
ENSG00000189050	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10851502	0.88[YRI][hapmap]
rs11070859	0.82[YRI][hapmap]
rs11070863	0.80[ASN][1000 genomes]
rs11631725	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634180	0.83[YRI][hapmap]
rs11634955	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11637716	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11638106	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12440990	0.89[YRI][hapmap]
rs1456299	0.93[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1456300	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054166	0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2124592	0.82[YRI][hapmap]
rs2124875	0.89[YRI][hapmap]
rs2305716	0.92[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2607119	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622775	0.94[JPT][hapmap]
rs2652594	0.87[JPT][hapmap]
rs28576876	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4774597	0.85[YRI][hapmap]
rs4775943	0.88[YRI][hapmap]
rs4775968	0.92[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55982453	0.82[ASN][1000 genomes]
rs60060794	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6493505	0.82[YRI][hapmap]
rs7167760	0.96[YRI][hapmap]
rs7170217	0.85[YRI][hapmap]
rs7170444	0.83[YRI][hapmap]
rs7170980	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7171884	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7174495	0.88[YRI][hapmap]
rs7183479	0.96[YRI][hapmap]
rs744039	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023455	0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8033234	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs8034197	0.80[ASN][1000 genomes]
rs8037340	0.80[ASN][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
rs11638154	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51965400-51969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:51965600-51972200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:51966600-51973400	Weak transcription	Right Atrium	heart
4	chr15:51967400-51973000	Weak transcription	K562	blood
5	chr15:51967800-51973000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:51968800-51973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:51969400-51969600	Enhancers	Brain Cingulate Gyrus	brain
8	chr15:51969400-51970200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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