Variant report

Variant	rs6493498
Chromosome Location	chr15:51754451-51754452
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	chr15:51753717..51756435-chr15:51759553..51761218,2	K562	blood:
2	chr15:51751987..51754955-chr15:51756566..51759249,2	MCF-7	breast:

Extended variants
information (count: 231 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:224)

rs_ID	r²[population]
rs10220909	0.90[EUR][1000 genomes]
rs1031664	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10438320	0.82[EUR][1000 genomes]
rs10467923	0.96[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10467924	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10519312	0.83[EUR][1000 genomes]
rs10519313	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1077361	0.84[EUR][1000 genomes]
rs10775144	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1080394	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs10851500	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10851502	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11070851	0.83[EUR][1000 genomes]
rs11070852	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070853	0.83[EUR][1000 genomes]
rs11070854	0.87[EUR][1000 genomes]
rs11070855	0.87[EUR][1000 genomes]
rs11070856	0.87[EUR][1000 genomes]
rs11070857	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs11070859	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11070860	0.84[EUR][1000 genomes]
rs11070862	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs11070863	0.81[EUR][1000 genomes]
rs11630336	0.82[EUR][1000 genomes]
rs11630743	0.88[EUR][1000 genomes]
rs11630842	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11631408	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11632853	0.82[EUR][1000 genomes]
rs11633395	0.83[EUR][1000 genomes]
rs11633713	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11634039	0.84[EUR][1000 genomes]
rs11634180	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11634999	0.85[EUR][1000 genomes]
rs11635216	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11635592	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11636170	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11638240	0.81[EUR][1000 genomes]
rs11855041	0.88[ASN][1000 genomes]
rs12050598	0.82[EUR][1000 genomes]
rs12050600	0.82[EUR][1000 genomes]
rs12101730	0.87[EUR][1000 genomes]
rs12101920	0.82[EUR][1000 genomes]
rs12102203	0.88[EUR][1000 genomes]
rs12372948	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12438892	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs12440990	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12441167	0.87[EUR][1000 genomes]
rs12441759	0.87[EUR][1000 genomes]
rs12442725	0.85[EUR][1000 genomes]
rs12442803	0.84[EUR][1000 genomes]
rs12442947	0.83[EUR][1000 genomes]
rs12443007	0.84[EUR][1000 genomes]
rs12592179	0.83[EUR][1000 genomes]
rs12592390	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs12592422	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs12592653	0.85[EUR][1000 genomes]
rs12592889	0.87[EUR][1000 genomes]
rs12593979	0.86[EUR][1000 genomes]
rs12908028	0.90[CHB][hapmap]
rs12913493	0.83[EUR][1000 genomes]
rs17524813	0.83[EUR][1000 genomes]
rs17603116	0.83[EUR][1000 genomes]
rs17609666	0.86[EUR][1000 genomes]
rs17609693	0.85[EUR][1000 genomes]
rs17609791	0.85[EUR][1000 genomes]
rs17609812	0.85[EUR][1000 genomes]
rs17609917	0.83[EUR][1000 genomes]
rs17609924	0.83[EUR][1000 genomes]
rs17648128	0.86[CHB][hapmap]
rs17704742	0.90[ASN][1000 genomes]
rs1902592	0.85[EUR][1000 genomes]
rs1902593	0.85[EUR][1000 genomes]
rs1902594	0.84[EUR][1000 genomes]
rs2124592	0.93[CEU][hapmap]
rs2124875	0.93[CEU][hapmap]
rs2124876	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2124877	0.84[EUR][1000 genomes]
rs2124878	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2124879	0.82[EUR][1000 genomes]
rs2278988	0.83[EUR][1000 genomes]
rs2278989	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2278990	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2305708	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2414104	0.88[ASN][1000 genomes]
rs2414105	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2414106	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2414108	0.83[ASN][1000 genomes]
rs2414109	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2414111	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2414113	0.84[EUR][1000 genomes]
rs2414114	0.84[EUR][1000 genomes]
rs2445746	0.81[CHB][hapmap]
rs2445751	0.83[CHB][hapmap]
rs2470192	0.86[CHB][hapmap]
rs2470194	0.87[CHB][hapmap]
rs28362471	0.93[ASN][1000 genomes]
rs28376817	0.84[EUR][1000 genomes]
rs28393906	0.85[EUR][1000 genomes]
rs28410165	0.85[EUR][1000 genomes]
rs28415556	0.86[EUR][1000 genomes]
rs28428679	0.83[EUR][1000 genomes]
rs28431083	0.83[EUR][1000 genomes]
rs28648597	0.87[EUR][1000 genomes]
rs28680710	0.83[EUR][1000 genomes]
rs28695624	0.85[EUR][1000 genomes]
rs28854610	0.83[EUR][1000 genomes]
rs28866855	0.84[EUR][1000 genomes]
rs28878886	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2899475	0.85[EUR][1000 genomes]
rs2899476	0.83[EUR][1000 genomes]
rs34604744	0.88[ASN][1000 genomes]
rs3736485	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4143721	0.85[EUR][1000 genomes]
rs4143722	0.80[EUR][1000 genomes]
rs4143723	0.85[EUR][1000 genomes]
rs4143724	0.85[EUR][1000 genomes]
rs4144941	0.88[EUR][1000 genomes]
rs4436729	0.84[ASN][1000 genomes]
rs4438255	0.84[EUR][1000 genomes]
rs4462537	0.81[EUR][1000 genomes]
rs4545756	0.85[EUR][1000 genomes]
rs4774589	0.87[EUR][1000 genomes]
rs4774591	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs4774592	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4774593	0.82[EUR][1000 genomes]
rs4774595	0.84[EUR][1000 genomes]
rs4774596	0.83[EUR][1000 genomes]
rs4774598	0.83[EUR][1000 genomes]
rs4775943	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775944	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4775945	0.95[CHB][hapmap];0.94[ASN][1000 genomes]
rs4775946	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4775950	0.88[ASN][1000 genomes]
rs4775951	0.87[EUR][1000 genomes]
rs4775952	0.85[EUR][1000 genomes]
rs4775953	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775955	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775956	0.85[EUR][1000 genomes]
rs4775958	0.84[EUR][1000 genomes]
rs4775959	0.84[EUR][1000 genomes]
rs4775960	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4775961	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4775963	0.84[EUR][1000 genomes]
rs4775965	0.83[EUR][1000 genomes]
rs4775966	0.83[EUR][1000 genomes]
rs4775967	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs55981933	0.83[EUR][1000 genomes]
rs56189052	0.82[EUR][1000 genomes]
rs62014659	0.82[EUR][1000 genomes]
rs62016017	0.84[EUR][1000 genomes]
rs6493499	0.83[EUR][1000 genomes]
rs6493500	0.83[EUR][1000 genomes]
rs6493501	0.82[EUR][1000 genomes]
rs6493502	0.88[ASN][1000 genomes]
rs6493503	0.82[EUR][1000 genomes]
rs6493504	0.88[ASN][1000 genomes]
rs6493505	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6493510	0.83[EUR][1000 genomes]
rs6493513	0.82[EUR][1000 genomes]
rs67524810	0.83[EUR][1000 genomes]
rs7161973	0.87[EUR][1000 genomes]
rs7162361	0.86[EUR][1000 genomes]
rs7162412	0.87[EUR][1000 genomes]
rs7162563	0.84[EUR][1000 genomes]
rs7165887	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7167760	0.96[CEU][hapmap]
rs7168546	0.84[EUR][1000 genomes]
rs7170217	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7170330	0.87[EUR][1000 genomes]
rs7170444	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7171439	0.87[EUR][1000 genomes]
rs7173880	0.88[EUR][1000 genomes]
rs7174435	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7174495	0.92[CEU][hapmap]
rs7176044	0.84[EUR][1000 genomes]
rs7176988	0.91[ASN][1000 genomes]
rs7177471	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7177720	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7181470	0.82[EUR][1000 genomes]
rs7182977	0.87[EUR][1000 genomes]
rs7183479	0.92[CEU][hapmap]
rs7495962	0.83[EUR][1000 genomes]
rs750162	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs750163	0.83[EUR][1000 genomes]
rs8023455	0.92[CEU][hapmap]
rs8024233	0.90[ASN][1000 genomes]
rs8024506	0.83[EUR][1000 genomes]
rs8025536	0.90[ASN][1000 genomes]
rs8028017	0.83[EUR][1000 genomes]
rs8030113	0.87[ASN][1000 genomes]
rs8030534	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8031903	0.86[EUR][1000 genomes]
rs8034340	0.96[CHB][hapmap];0.94[ASN][1000 genomes]
rs8035135	0.83[EUR][1000 genomes]
rs8036609	0.87[EUR][1000 genomes]
rs8036821	0.87[EUR][1000 genomes]
rs8036904	0.87[EUR][1000 genomes]
rs8037167	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs8037340	0.80[EUR][1000 genomes]
rs8037840	0.87[EUR][1000 genomes]
rs8038101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8038203	0.85[EUR][1000 genomes]
rs8038341	0.80[EUR][1000 genomes]
rs8039073	0.86[EUR][1000 genomes]
rs8039835	0.84[EUR][1000 genomes]
rs8040080	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs8040538	0.84[EUR][1000 genomes]
rs8040648	0.81[EUR][1000 genomes]
rs8041197	0.82[EUR][1000 genomes]
rs8041514	0.86[EUR][1000 genomes]
rs8042221	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8042289	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs8042840	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs882385	0.85[EUR][1000 genomes]
rs882386	0.81[EUR][1000 genomes]
rs898135	0.91[CHB][hapmap]
rs930919	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs930920	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9708186	0.84[EUR][1000 genomes]
rs9920124	0.84[EUR][1000 genomes]
rs9920145	0.84[EUR][1000 genomes]
rs9944241	0.96[CEU][hapmap]
rs9944259	0.84[EUR][1000 genomes]
rs9944264	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
rs6493498	DMXL2	cis	multi-tissue	Pritchard
rs6493498	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51737000-51775600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr15:51737000-51776400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:51737600-51762400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:51737800-51758400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:51737800-51762400	Weak transcription	Colonic Mucosa	Colon
6	chr15:51738000-51755400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:51738200-51784600	Weak transcription	Stomach Mucosa	stomach
8	chr15:51738400-51777400	Weak transcription	Small Intestine	intestine
9	chr15:51739000-51776000	Weak transcription	Gastric	stomach
10	chr15:51740800-51775200	Weak transcription	Pancreas	Pancrea
11	chr15:51742400-51764800	Weak transcription	Primary B cells from cord blood	blood
12	chr15:51742400-51775800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:51742600-51762000	Weak transcription	Spleen	Spleen
14	chr15:51742600-51762200	Weak transcription	Aorta	Aorta
15	chr15:51742600-51775400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:51742600-51775400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:51742600-51776000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:51742600-51776600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:51742600-51776800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:51743000-51774200	Weak transcription	HMEC	breast
21	chr15:51743000-51775200	Weak transcription	HSMMtube	muscle
22	chr15:51743000-51780200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:51743600-51769600	Weak transcription	HSMM	muscle
24	chr15:51745800-51755200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:51747800-51762200	Weak transcription	Primary T cells from cord blood	blood
26	chr15:51748000-51776400	Weak transcription	Right Ventricle	heart
27	chr15:51748200-51774400	Weak transcription	Fetal Heart	heart
28	chr15:51748400-51758000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:51748400-51762200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:51749000-51776600	Weak transcription	Fetal Kidney	kidney
31	chr15:51749200-51762000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:51749200-51772800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:51749200-51775400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:51749200-51777400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:51749400-51762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:51749400-51762200	Weak transcription	Lung	lung
37	chr15:51749600-51762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:51749600-51762200	Weak transcription	Fetal Stomach	stomach
39	chr15:51749600-51762400	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:51749600-51765200	Weak transcription	Thymus	Thymus
41	chr15:51749600-51775000	Weak transcription	Fetal Intestine Small	intestine
42	chr15:51749800-51762000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:51749800-51762000	Weak transcription	GM12878-XiMat	blood
44	chr15:51750400-51770000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:51750400-51775400	Weak transcription	Brain Substantia Nigra	brain
46	chr15:51750800-51761400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:51750800-51776200	Weak transcription	NHDF-Ad	bronchial
48	chr15:51750800-51776600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:51750800-51777400	Weak transcription	Osteobl	bone
50	chr15:51751000-51762000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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