Variant report

Variant	rs241932
Chromosome Location	chr19:38256696-38256697
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38256038..38258477-chr19:38258531..38260725,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10048511	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10401968	0.82[EUR][1000 genomes]
rs10402530	0.83[EUR][1000 genomes]
rs10403173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs10404567	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs10408619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10409402	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10409487	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420891	0.83[EUR][1000 genomes]
rs11083432	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs1119229	0.88[CEU][hapmap]
rs11673023	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11878269	0.82[EUR][1000 genomes]
rs11879180	0.83[EUR][1000 genomes]
rs1291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975057	0.83[EUR][1000 genomes]
rs12979640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[ASN][1000 genomes]
rs13744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs16958861	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16958863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs171376	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725499	0.88[CEU][hapmap]
rs1974714	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1975937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2075281	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs2075284	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2287229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs241933	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241950	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2909085	0.82[ASN][1000 genomes]
rs2909088	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs2909093	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2909098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2909100	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs2909105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs2909109	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2927739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2927740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs2927746	0.81[ASN][1000 genomes]
rs2927747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs2972430	0.81[ASN][1000 genomes]
rs2972434	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972445	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972448	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs3095724	0.85[ASN][1000 genomes]
rs3095726	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112434	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap]
rs353415	1.00[CEU][hapmap]
rs353423	1.00[CEU][hapmap]
rs3786869	0.87[CEU][hapmap]
rs3829688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs3848626	0.81[EUR][1000 genomes]
rs4239516	0.87[CEU][hapmap]
rs4802135	0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs4803262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4803509	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803524	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs56151076	0.81[ASN][1000 genomes]
rs6508736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs6508742	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs705491	0.88[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs705493	0.88[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs705495	0.88[CEU][hapmap]
rs7250409	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs7257125	0.82[EUR][1000 genomes]
rs8101752	0.81[EUR][1000 genomes]
rs8101858	0.80[EUR][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs8103633	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104076	0.82[EUR][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8112706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.83[EUR][1000 genomes]
rs833926	1.00[CEU][hapmap]
rs856300	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304569	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958305	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs968073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs241932	ZNF571	cis	multi-tissue	Pritchard
rs241932	CBLC	cis	parietal	SCAN
rs241932	PHLDB3	cis	cerebellum	SCAN
rs241932	PAFAH1B3	cis	cerebellum	SCAN
rs241932	HIPK4	cis	cerebellum	SCAN
rs241932	WDR87	cis	Thyroid	GTEx
rs241932	PHLDB3	cis	parietal	SCAN
rs241932	DMPK	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
2	chr19:38231000-38258200	Weak transcription	Brain Anterior Caudate	brain
3	chr19:38231000-38258400	Weak transcription	Fetal Kidney	kidney
4	chr19:38231000-38258800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:38231800-38257600	Weak transcription	HSMM	muscle
9	chr19:38231800-38258200	Weak transcription	HSMMtube	muscle
10	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
11	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
12	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
14	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
15	chr19:38239400-38257400	Weak transcription	Brain Angular Gyrus	brain
16	chr19:38242200-38258400	Weak transcription	NHDF-Ad	bronchial
17	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:38243000-38258200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:38243600-38257200	Weak transcription	Fetal Lung	lung
20	chr19:38245200-38258200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:38246200-38258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:38246800-38259600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:38246800-38259800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:38247400-38258200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:38247400-38259800	Weak transcription	Placenta	Placenta
26	chr19:38247800-38260000	Weak transcription	Osteobl	bone
27	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
28	chr19:38248400-38264600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr19:38248800-38269400	Weak transcription	NH-A	brain
30	chr19:38249000-38259000	Weak transcription	Thymus	Thymus
31	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
32	chr19:38249400-38258200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:38250400-38259600	Weak transcription	Esophagus	oesophagus
35	chr19:38250600-38262600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:38250600-38264000	Strong transcription	Primary T cells from cord blood	blood
37	chr19:38250600-38264400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr19:38250600-38265000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:38250600-38266400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:38250800-38261400	Strong transcription	Fetal Stomach	stomach
41	chr19:38251000-38258400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr19:38251000-38259600	Weak transcription	Brain Germinal Matrix	brain
43	chr19:38251200-38258800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:38251400-38261200	Strong transcription	Fetal Muscle Leg	muscle
45	chr19:38251800-38269400	Weak transcription	Gastric	stomach
46	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
47	chr19:38252200-38259600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:38252600-38269000	Weak transcription	NHEK	skin
50	chr19:38252800-38257200	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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