Variant report

Variant	rs9944241
Chromosome Location	chr15:51898058-51898059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51896366..51899054-chr15:52579042..52581024,2	MCF-7	breast:
2	chr15:51893271..51898734-chr15:51911463..51916763,7	K562	blood:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1031664	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs10467923	0.92[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap]
rs10519313	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10775144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1080394	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs10851502	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap]
rs11070857	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap]
rs11070859	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11070862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs11630842	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs11631408	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs11633713	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11634180	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11635216	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs11635592	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11636170	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12372948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs12438892	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[YRI][hapmap]
rs12440990	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[YRI][hapmap]
rs2124592	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs2124875	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[YRI][hapmap]
rs2124876	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2124878	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2124879	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2278989	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2278990	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2305708	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs2305716	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2414105	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs2414106	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2414109	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2414111	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs2607119	0.81[GIH][hapmap]
rs3736485	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs4774590	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4774591	0.92[CEU][hapmap]
rs4774597	0.82[CHB][hapmap];0.84[YRI][hapmap]
rs4775943	0.92[CEU][hapmap];0.88[YRI][hapmap]
rs4775944	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4775946	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4775953	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4775955	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4775960	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4775961	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs4775968	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs6493498	0.96[CEU][hapmap]
rs6493505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7165887	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs7167760	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs7170217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7170444	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7170980	0.81[CEU][hapmap];0.95[TSI][hapmap]
rs7174435	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7174495	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap]
rs7177471	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs7177720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7183479	0.92[CEU][hapmap];0.81[YRI][hapmap]
rs744039	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs750162	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs8023455	0.92[CEU][hapmap]
rs8037167	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8040080	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs8042221	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs8042289	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8042840	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs930920	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv569408	chr15:51867172-51946100	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a
6	esv3311227	chr15:51897590-51898150	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	esv3336333	chr15:51897597-51898165	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3311231	chr15:51897639-51898114	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	esv3311228	chr15:51897641-51898079	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	esv3399634	chr15:51897646-51898093	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	esv3494379	chr15:51897648-51898173	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv3494378	chr15:51897654-51898166	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	esv3494380	chr15:51897654-51898166	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv3699	chr15:51897658-51898316	Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	esv3311229	chr15:51897661-51898106	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9944241	DMXL2	Cis_1M	lymphoblastoid	RTeQTL
rs9944241	SCG3	cis	cerebellum	SCAN
rs9944241	DMXL2	cis	multi-tissue	Pritchard
rs9944241	DMXL2	cis	lymphoblastoid	seeQTL
rs9944241	ARPP19	cis	parietal	SCAN
rs9944241	BCL2L10	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51889400-51909400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:51890000-51902000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:51891800-51903800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:51892600-51913000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:51893000-51911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:51893800-51904000	Weak transcription	Fetal Stomach	stomach
7	chr15:51894000-51906000	Weak transcription	Dnd41	blood
8	chr15:51894800-51901600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr15:51895000-51911600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:51895200-51913000	Weak transcription	HMEC	breast
11	chr15:51896000-51904000	Weak transcription	Lung	lung
12	chr15:51897200-51910800	Weak transcription	A549	lung
13	chr15:51898000-51898400	Strong transcription	Monocytes-CD14+_RO01746	blood

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