Variant report

Variant	rs705494
Chromosome Location	chr19:38426036-38426037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
2	chr19:38424879..38427033-chr19:38465266..38467452,2	MCF-7	breast:
3	chr19:38423922..38426366-chr19:38436893..38438716,2	MCF-7	breast:
4	chr19:38423743..38426556-chr19:38482738..38484356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10401637	0.84[EUR][1000 genomes]
rs10402530	0.81[EUR][1000 genomes]
rs10404567	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10420891	0.81[EUR][1000 genomes]
rs10427125	0.81[EUR][1000 genomes]
rs1119229	0.88[CEU][hapmap]
rs11879180	0.81[EUR][1000 genomes]
rs1291	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[TSI][hapmap]
rs12974225	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs12975057	0.81[EUR][1000 genomes]
rs1643462	0.86[EUR][1000 genomes]
rs1643463	0.86[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643467	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643469	0.89[EUR][1000 genomes]
rs1725477	0.86[EUR][1000 genomes]
rs1725478	0.86[EUR][1000 genomes]
rs1725480	0.86[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1725483	0.86[EUR][1000 genomes]
rs1725485	0.86[EUR][1000 genomes]
rs1725487	0.86[EUR][1000 genomes]
rs1725488	0.85[EUR][1000 genomes]
rs1725494	0.88[EUR][1000 genomes]
rs1725499	0.88[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs241932	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2544718	0.88[EUR][1000 genomes]
rs3095726	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs35209753	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs353398	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353399	0.91[EUR][1000 genomes]
rs353400	0.91[EUR][1000 genomes]
rs353402	0.91[EUR][1000 genomes]
rs353403	0.89[EUR][1000 genomes]
rs353404	0.91[EUR][1000 genomes]
rs353407	0.91[EUR][1000 genomes]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353415	1.00[CEU][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs353416	0.91[EUR][1000 genomes]
rs353417	0.91[EUR][1000 genomes]
rs353419	0.91[EUR][1000 genomes]
rs353420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs353421	0.91[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs353424	0.91[EUR][1000 genomes]
rs353425	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs353426	0.89[EUR][1000 genomes]
rs353427	0.91[EUR][1000 genomes]
rs353428	0.86[EUR][1000 genomes]
rs353429	0.84[EUR][1000 genomes]
rs353430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3786869	0.87[CEU][hapmap]
rs4239516	0.87[CEU][hapmap]
rs4802135	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4803524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4803551	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs4803573	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705491	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs705493	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705495	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705500	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7250409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250571	0.84[EUR][1000 genomes]
rs7250868	0.84[EUR][1000 genomes]
rs7252010	0.83[EUR][1000 genomes]
rs7258597	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs752878	0.86[EUR][1000 genomes]
rs8101858	0.81[EUR][1000 genomes]
rs8102579	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs8107341	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8112706	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.81[EUR][1000 genomes]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs833896	0.85[EUR][1000 genomes]
rs833897	0.86[EUR][1000 genomes]
rs833898	0.86[EUR][1000 genomes]
rs833914	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs833926	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs856300	0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs856304	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs9304572	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1820125	chr19:38424904-38427984	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs705494	DMPK	cis	parietal	SCAN
rs705494	CBLC	cis	parietal	SCAN
rs705494	PAFAH1B3	cis	cerebellum	SCAN
rs705494	PHLDB3	cis	cerebellum	SCAN
rs705494	ZNF571	cis	multi-tissue	Pritchard
rs705494	WDR87	cis	Thyroid	GTEx
rs705494	AXL	cis	cerebellum	SCAN
rs705494	PHLDB3	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
5	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
6	chr19:38423200-38426200	Weak transcription	Ovary	ovary
7	chr19:38423200-38426600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:38423400-38426400	Weak transcription	Brain Germinal Matrix	brain
10	chr19:38423400-38427600	Enhancers	Liver	Liver
11	chr19:38423400-38433800	Weak transcription	Thymus	Thymus
12	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:38424400-38426400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:38424400-38426800	Weak transcription	Fetal Brain Female	brain
15	chr19:38424400-38427000	Enhancers	Gastric	stomach
16	chr19:38424400-38428000	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr19:38424600-38426200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:38424600-38426200	Weak transcription	Lung	lung
19	chr19:38424600-38429600	ZNF genes & repeats	GM12878-XiMat	blood
20	chr19:38424600-38438800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:38424600-38439200	Weak transcription	Spleen	Spleen
22	chr19:38424800-38426200	Weak transcription	Fetal Lung	lung
23	chr19:38424800-38426200	Weak transcription	HUVEC	blood vessel
24	chr19:38424800-38427200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:38424800-38428000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
27	chr19:38425000-38426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:38425000-38426200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:38425000-38426200	Weak transcription	Colonic Mucosa	Colon
30	chr19:38425000-38426200	Weak transcription	Right Atrium	heart
31	chr19:38425000-38426600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr19:38425000-38429000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38425000-38431200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:38425000-38431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:38425000-38432200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:38425000-38438400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:38425000-38441000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
39	chr19:38425200-38436000	Enhancers	Stomach Mucosa	stomach
40	chr19:38425400-38426600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr19:38425400-38427800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr19:38425400-38430200	ZNF genes & repeats	A549	lung
43	chr19:38425600-38426200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:38425600-38426200	Strong transcription	Osteobl	bone
45	chr19:38425600-38426800	ZNF genes & repeats	Brain Anterior Caudate	brain
46	chr19:38425800-38426200	Weak transcription	Fetal Heart	heart
47	chr19:38425800-38426200	Weak transcription	Pancreas	Pancrea
48	chr19:38425800-38426200	Weak transcription	HMEC	breast
49	chr19:38425800-38426400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr19:38425800-38427000	ZNF genes & repeats	Fetal Muscle Leg	muscle

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