Variant report

Variant	rs17524750
Chromosome Location	chr15:51780722-51780723
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	chr15:51773834..51778249-chr15:51779820..51782019,4	K562	blood:
2	chr15:51776385..51778052-chr15:51779889..51781997,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1017679	0.90[CEU][hapmap]
rs10851501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070861	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11857716	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12324531	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12708427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12901452	0.82[EUR][1000 genomes]
rs12904173	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12904583	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378892	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1378893	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1378894	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1378895	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1456295	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1456297	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1471072	0.90[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1551657	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17524906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1840707	0.95[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1902595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1902596	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061425	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2252220	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2414112	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2445754	0.85[AFR][1000 genomes]
rs2446407	0.95[CEU][hapmap]
rs2459397	1.00[JPT][hapmap]
rs2459399	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs2470167	0.83[AMR][1000 genomes]
rs2470193	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2606134	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2606136	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2606137	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2606138	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2606139	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2606141	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2606143	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2606145	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2606146	0.82[EUR][1000 genomes]
rs2607110	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2607112	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2607116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622768	0.82[EUR][1000 genomes]
rs2622769	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622770	0.95[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs28408214	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34448759	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34532503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34662965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34929849	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35011964	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35561856	0.85[EUR][1000 genomes]
rs35859241	0.82[AMR][1000 genomes]
rs3751585	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4465557	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4774594	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4775954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55725532	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56879579	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61618680	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6493507	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493511	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493514	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs716986	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7180329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8025974	0.82[EUR][1000 genomes]
rs8026587	0.90[CEU][hapmap];0.82[MEX][hapmap]
rs8027162	0.82[EUR][1000 genomes]
rs8029731	0.82[EUR][1000 genomes]
rs897581	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs956171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9672605	0.82[EUR][1000 genomes]
rs9944266	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	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
4	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv904218	chr15:51743186-51873407	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17524750	DMXL2	cis	cerebellum	SCAN
rs17524750	KIAA1370	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51738200-51784600	Weak transcription	Stomach Mucosa	stomach
2	chr15:51763600-51826800	Weak transcription	Colonic Mucosa	Colon
3	chr15:51763800-51782000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:51763800-51784000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:51773000-51782000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:51775000-51784800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:51776600-51800000	Weak transcription	Esophagus	oesophagus
8	chr15:51776800-51784200	Weak transcription	Pancreas	Pancrea
9	chr15:51776800-51787200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:51776800-51790200	Weak transcription	Lung	lung
11	chr15:51776800-51790800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:51776800-51793800	Weak transcription	Fetal Stomach	stomach
13	chr15:51776800-51797200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:51776800-51801600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:51776800-51815600	Weak transcription	Aorta	Aorta
16	chr15:51776800-51837600	Weak transcription	Fetal Thymus	thymus
17	chr15:51776800-51855200	Weak transcription	Thymus	Thymus
18	chr15:51777200-51781200	Strong transcription	Placenta	Placenta
19	chr15:51777600-51819000	Weak transcription	Small Intestine	intestine
20	chr15:51777800-51780800	Strong transcription	Brain Germinal Matrix	brain
21	chr15:51777800-51781200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:51777800-51781600	Strong transcription	Liver	Liver
23	chr15:51777800-51786600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:51777800-51786600	Weak transcription	NHLF	lung
25	chr15:51777800-51786800	Weak transcription	Primary T cells from cord blood	blood
26	chr15:51777800-51787000	Weak transcription	HMEC	breast
27	chr15:51777800-51790200	Weak transcription	Fetal Brain Male	brain
28	chr15:51777800-51792200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:51777800-51795200	Weak transcription	Spleen	Spleen
30	chr15:51777800-51799600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:51778200-51781800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:51778200-51781800	Strong transcription	Fetal Intestine Large	intestine
33	chr15:51778200-51811200	Weak transcription	NHDF-Ad	bronchial
34	chr15:51778400-51781200	Strong transcription	Adipose Nuclei	Adipose
35	chr15:51778400-51781400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:51778400-51782800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:51778400-51783000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:51778400-51784000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:51778400-51784600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr15:51778400-51784800	Weak transcription	HUVEC	blood vessel
41	chr15:51778400-51790200	Weak transcription	Left Ventricle	heart
42	chr15:51778400-51790600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:51778400-51794400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:51778400-51825800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:51778600-51785200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr15:51778600-51785600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:51778600-51790200	Weak transcription	HSMMtube	muscle
48	chr15:51778600-51790800	Weak transcription	Fetal Heart	heart
49	chr15:51778600-51791000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:51778600-51791200	Weak transcription	Brain Substantia Nigra	brain

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