Variant report

Variant	rs705495
Chromosome Location	chr19:38426985-38426986
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	chr19:38426351..38429541-chr19:38429679..38432396,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10404159	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs10415399	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420746	0.88[CEU][hapmap]
rs11083441	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs12608883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1291	0.88[CEU][hapmap]
rs12973580	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.84[EUR][1000 genomes]
rs1643461	0.88[EUR][1000 genomes]
rs1643466	0.87[CEU][hapmap]
rs1643467	0.87[CEU][hapmap]
rs1643468	0.87[CEU][hapmap]
rs1725481	0.88[CEU][hapmap]
rs1725482	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs1725499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075281	0.88[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095726	0.82[CEU][hapmap]
rs353410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353414	0.87[CEU][hapmap]
rs353415	0.88[CEU][hapmap]
rs353423	0.87[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865514	1.00[YRI][hapmap]
rs4239516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802144	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802151	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705492	0.88[CEU][hapmap]
rs705493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705499	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109053	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109835	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110284	0.87[CEU][hapmap]
rs8112706	0.87[CEU][hapmap]
rs8113273	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs833895	0.87[CEU][hapmap]
rs833926	0.88[CEU][hapmap]
rs856300	0.82[CEU][hapmap]
rs856304	0.88[CEU][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs705495	PAFAH1B3	cis	cerebellum	SCAN
rs705495	PHLDB3	cis	parietal	SCAN
rs705495	PHLDB3	cis	cerebellum	SCAN
rs705495	CBLC	cis	parietal	SCAN
rs705495	HIF3A	cis	parietal	SCAN
rs705495	AC012309.5	cis	Artery Tibial	GTEx
rs705495	DMPK	cis	parietal	SCAN

Chromatin state (count:89 , 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	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:38423400-38427600	Enhancers	Liver	Liver
6	chr19:38423400-38433800	Weak transcription	Thymus	Thymus
7	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:38424400-38427000	Enhancers	Gastric	stomach
9	chr19:38424400-38428000	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr19:38424600-38429600	ZNF genes & repeats	GM12878-XiMat	blood
11	chr19:38424600-38438800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:38424600-38439200	Weak transcription	Spleen	Spleen
13	chr19:38424800-38427200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr19:38424800-38428000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
16	chr19:38425000-38429000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38425000-38431200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:38425000-38431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:38425000-38432200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:38425000-38438400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:38425000-38441000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
23	chr19:38425200-38436000	Enhancers	Stomach Mucosa	stomach
24	chr19:38425400-38427800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr19:38425400-38430200	ZNF genes & repeats	A549	lung
26	chr19:38425800-38427000	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr19:38425800-38429600	Enhancers	Fetal Intestine Large	intestine
28	chr19:38425800-38430600	Weak transcription	Small Intestine	intestine
29	chr19:38426000-38427000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr19:38426000-38427000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:38426000-38427000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:38426000-38427000	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr19:38426000-38427000	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr19:38426000-38427000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:38426000-38427000	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr19:38426000-38427000	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:38426000-38427000	ZNF genes & repeats	Psoas Muscle	Psoas
38	chr19:38426000-38427000	ZNF genes & repeats	HSMM	muscle
39	chr19:38426000-38427200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr19:38426000-38427200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:38426000-38427200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:38426000-38427200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr19:38426000-38427400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
44	chr19:38426000-38427600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
45	chr19:38426000-38427600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr19:38426000-38427800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
47	chr19:38426200-38427000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:38426200-38427000	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr19:38426200-38427000	ZNF genes & repeats	Lung	lung
50	chr19:38426200-38427000	ZNF genes & repeats	Right Atrium	heart

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