Variant report

Variant	rs1725499
Chromosome Location	chr19:38430140-38430141
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38396824..38398829-chr19:38427494..38430432,2	MCF-7	breast:
2	chr19:38426351..38429541-chr19:38429679..38432396,3	MCF-7	breast:
3	chr19:38427297..38430730-chr19:38431010..38433796,3	K562	blood:
4	chr19:38395808..38398765-chr19:38427485..38430448,3	MCF-7	breast:
5	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
6	chr19:38429620..38432049-chr19:38435086..38437572,3	K562	blood:
7	chr19:38421583..38424887-chr19:38429672..38432254,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10404159	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap]
rs10415399	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[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];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420746	0.83[CEU][hapmap]
rs11083441	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12608883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12973580	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.85[EUR][1000 genomes]
rs1643461	0.89[EUR][1000 genomes]
rs1643466	0.82[CEU][hapmap]
rs1643467	0.83[CEU][hapmap]
rs1643468	0.83[CEU][hapmap]
rs1725481	0.83[CEU][hapmap]
rs1725482	0.88[CEU][hapmap]
rs2075281	0.83[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353414	0.83[CEU][hapmap]
rs353415	0.83[CEU][hapmap]
rs353423	0.83[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802144	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802151	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705492	0.83[CEU][hapmap]
rs705493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap]
rs705495	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]
rs705499	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109053	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109835	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110284	0.83[CEU][hapmap]
rs8112706	0.83[CEU][hapmap]
rs8113273	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs833895	0.83[CEU][hapmap]
rs833926	0.83[CEU][hapmap]
rs856300	0.82[CEU][hapmap]
rs856304	0.88[CEU][hapmap]

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	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	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1725499	AC012309.5	cis	Artery Tibial	GTEx

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	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:38423400-38433800	Weak transcription	Thymus	Thymus
6	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:38424600-38438800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:38424600-38439200	Weak transcription	Spleen	Spleen
9	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
10	chr19:38425000-38431200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:38425000-38431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:38425000-38432200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:38425000-38438400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr19:38425000-38441000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
16	chr19:38425200-38436000	Enhancers	Stomach Mucosa	stomach
17	chr19:38425400-38430200	ZNF genes & repeats	A549	lung
18	chr19:38425800-38430600	Weak transcription	Small Intestine	intestine
19	chr19:38426400-38432200	Weak transcription	NH-A	brain
20	chr19:38426400-38435600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:38426600-38430200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:38426600-38435000	Weak transcription	HUVEC	blood vessel
24	chr19:38426600-38438200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:38426600-38442600	Weak transcription	HMEC	breast
26	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:38426600-38450800	Weak transcription	Ovary	ovary
28	chr19:38426800-38431800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:38426800-38438400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:38426800-38439400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:38426800-38441000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:38427000-38431200	Weak transcription	Gastric	stomach
34	chr19:38427000-38433800	Weak transcription	Right Atrium	heart
35	chr19:38427000-38438600	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:38427000-38438600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:38427000-38439400	Weak transcription	Lung	lung
38	chr19:38427000-38441000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:38427000-38441000	Weak transcription	Brain Germinal Matrix	brain
40	chr19:38427000-38441200	Weak transcription	Adipose Nuclei	Adipose
41	chr19:38427000-38441200	Weak transcription	Left Ventricle	heart
42	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
44	chr19:38427200-38433800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:38427200-38438400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:38427200-38443800	Weak transcription	NHEK	skin
47	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:38427400-38431400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:38427400-38431600	Weak transcription	Pancreas	Pancrea
50	chr19:38427400-38432200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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