Variant report

Variant	rs1402325
Chromosome Location	chr19:44105736-44105737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44105666..44109399-chr19:44121081..44124426,3	K562	blood:
2	chr19:44099419..44102216-chr19:44103629..44105771,4	MCF-7	breast:
3	chr19:44105250..44107981-chr19:44110094..44113502,4	K562	blood:

Variant related genes	Relation type
ENSG00000131116	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11083712	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11671645	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1402326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17655484	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs17655574	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1879387	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2003098	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2302421	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3213248	0.80[AFR][1000 genomes]
rs3213266	0.81[LWK][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs3213271	0.80[AFR][1000 genomes]
rs3213328	0.84[YRI][hapmap]
rs3746002	0.85[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3746003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815422	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803643	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4803644	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73038867	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767540	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs880108	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs939461	0.81[LWK][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1402325	LOC653583	cis	multi-tissue	Pritchard
rs1402325	PLAUR	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44101600-44112000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44101800-44109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:44101800-44111600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:44101800-44123200	Weak transcription	Small Intestine	intestine
5	chr19:44102000-44122600	Weak transcription	Fetal Kidney	kidney
6	chr19:44102200-44111000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:44102200-44111200	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:44102200-44113600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:44102200-44114200	Weak transcription	NH-A	brain
10	chr19:44102200-44114600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:44102200-44122600	Weak transcription	Psoas Muscle	Psoas
12	chr19:44102400-44106000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:44102400-44106200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:44102400-44107200	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:44102400-44107400	Strong transcription	Primary T cells from cord blood	blood
16	chr19:44102400-44107400	Strong transcription	Placenta	Placenta
17	chr19:44102400-44109600	Weak transcription	Fetal Brain Male	brain
18	chr19:44102400-44110800	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:44102400-44119600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:44102400-44122600	Weak transcription	NHDF-Ad	bronchial
21	chr19:44102600-44105800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:44102600-44105800	Strong transcription	Brain Germinal Matrix	brain
23	chr19:44102600-44106000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:44102600-44106000	Strong transcription	Fetal Lung	lung
25	chr19:44102600-44106600	Weak transcription	HSMMtube	muscle
26	chr19:44102600-44106800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:44102600-44106800	Strong transcription	Fetal Intestine Small	intestine
28	chr19:44102600-44106800	Weak transcription	Stomach Mucosa	stomach
29	chr19:44102600-44107000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr19:44102600-44107200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:44102600-44107200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:44102600-44107200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:44102600-44107200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:44102600-44107200	Strong transcription	Left Ventricle	heart
35	chr19:44102600-44107200	Strong transcription	Lung	lung
36	chr19:44102600-44107400	Strong transcription	Fetal Intestine Large	intestine
37	chr19:44102600-44107400	Strong transcription	Fetal Thymus	thymus
38	chr19:44102600-44108000	Strong transcription	Thymus	Thymus
39	chr19:44102600-44108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:44102600-44109800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:44102600-44115800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:44102600-44116200	Weak transcription	Hela-S3	cervix
43	chr19:44102600-44120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:44102600-44121200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:44102600-44122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:44102600-44122600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:44102800-44106200	Strong transcription	Fetal Brain Female	brain
48	chr19:44102800-44106200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr19:44102800-44106800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:44102800-44107200	Strong transcription	Primary B cells from peripheral blood	blood

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