Variant report

Variant	rs3213564
Chromosome Location	chr1:172349921-172349922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172348750..172351497-chr1:172354142..172356415,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-2	chr1:172349883-172350046	NONHSAT007610

Variant related genes	Relation type
ENSG00000197959	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1011731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1023479	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10752943	0.95[ASN][1000 genomes]
rs10752944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10797996	0.97[ASN][1000 genomes]
rs10911654	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10911681	0.95[ASN][1000 genomes]
rs10911684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10911792	0.90[CHB][hapmap]
rs12404665	0.97[ASN][1000 genomes]
rs12405515	0.90[ASN][1000 genomes]
rs1894633	0.83[ASW][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2001127	0.93[ASN][1000 genomes]
rs2001128	0.93[ASN][1000 genomes]
rs2001129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2213732	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2227198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2227199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2227200	0.95[ASN][1000 genomes]
rs2269612	0.97[ASN][1000 genomes]
rs2301453	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3768445	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4504922	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4916251	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916252	0.97[ASN][1000 genomes]
rs4916253	0.93[ASN][1000 genomes]
rs4916254	0.86[ASN][1000 genomes]
rs4916263	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916264	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916265	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs57668887	0.80[ASN][1000 genomes]
rs6424894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6676665	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6700575	0.95[ASN][1000 genomes]
rs714515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73046851	0.83[ASN][1000 genomes]
rs7517737	0.93[ASN][1000 genomes]
rs7518039	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7539464	0.93[ASN][1000 genomes]
rs7539972	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7544610	0.97[ASN][1000 genomes]
rs7546252	0.93[ASN][1000 genomes]
rs9286854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.89[CHB][hapmap]
rs9425297	0.92[ASN][1000 genomes]
rs9425298	0.93[ASN][1000 genomes]
rs9425299	0.93[ASN][1000 genomes]
rs9425300	0.93[ASN][1000 genomes]
rs9425301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425573	0.82[ASN][1000 genomes]
rs9425575	0.83[ASN][1000 genomes]
rs9425579	0.98[ASN][1000 genomes]
rs9425586	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425587	0.97[ASN][1000 genomes]
rs9425589	0.97[ASN][1000 genomes]
rs9425590	0.90[ASN][1000 genomes]
rs9425591	0.93[ASN][1000 genomes]
rs9425592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425628	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs991790	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172343600-172352200	Weak transcription	HSMM	muscle
2	chr1:172343600-172359800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:172344800-172352400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:172344800-172357800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:172344800-172359000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:172345600-172350200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:172345800-172351200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:172345800-172352200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:172346400-172351000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:172346600-172367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:172347400-172357600	Weak transcription	Brain Substantia Nigra	brain
12	chr1:172348000-172350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:172348000-172351200	Weak transcription	NHDF-Ad	bronchial
14	chr1:172348000-172351600	Weak transcription	Ovary	ovary
15	chr1:172348200-172351600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:172348400-172350400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:172348600-172350000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:172348600-172351800	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:172348600-172353600	Enhancers	Fetal Lung	lung
20	chr1:172348800-172350200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:172349200-172350400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:172349400-172350000	Flanking Active TSS	GM12878-XiMat	blood
23	chr1:172349400-172351400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:172349600-172350000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:172349600-172350000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr1:172349600-172350000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr1:172349600-172350000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr1:172349600-172350000	Enhancers	Thymus	Thymus
29	chr1:172349600-172350400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:172349600-172350400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr1:172349600-172350400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:172349600-172350400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:172349600-172350600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:172349600-172350600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:172349600-172350600	Flanking Active TSS	Dnd41	blood
36	chr1:172349600-172351800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:172349600-172352200	Enhancers	Colon Smooth Muscle	Colon
38	chr1:172349600-172353600	Enhancers	Fetal Stomach	stomach
39	chr1:172349600-172353800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:172349600-172356400	Enhancers	Fetal Kidney	kidney
41	chr1:172349600-172362000	Weak transcription	Left Ventricle	heart
42	chr1:172349800-172350000	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr1:172349800-172350000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:172349800-172350000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:172349800-172350200	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr1:172349800-172350200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:172349800-172350200	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:172349800-172350200	Enhancers	Osteobl	bone
49	chr1:172349800-172350400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr1:172349800-172350400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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