Variant report

Variant	rs6425512
Chromosome Location	chr1:179000143-179000144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:178998854..179000742-chr1:179002565..179004439,2	MCF-7	breast:
2	chr1:178969379..178972157-chr1:178998248..179000443,2	MCF-7	breast:
3	chr1:178980100..178983059-chr1:178999156..179001335,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10082052	0.86[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1046385	1.00[ASW][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs10798649	0.81[JPT][hapmap]
rs10913672	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581232	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1325194	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs2025584	0.84[JPT][hapmap]
rs2182102	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2296377	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[AMR][1000 genomes]
rs2636266	1.00[ASW][hapmap]
rs2636290	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs2793805	1.00[ASW][hapmap]
rs28913887	1.00[YRI][hapmap]
rs28913889	1.00[YRI][hapmap]
rs3753533	0.81[JPT][hapmap]
rs3813638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818433	1.00[ASW][hapmap]
rs3820163	0.81[JPT][hapmap]
rs4360489	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4652344	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4652348	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425515	0.86[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs6697029	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7532578	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538498	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544801	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6425512	RALGPS2	cis	parietal	SCAN
rs6425512	TOR3A	cis	Artery Tibial	GTEx
rs6425512	GPR52	cis	parietal	SCAN
rs6425512	FAM20B	cis	parietal	SCAN
rs6425512	FAM20B	cis	cerebellum	SCAN
rs6425512	ABL2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178996200-179001200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:178996200-179003200	Weak transcription	Gastric	stomach
3	chr1:178996200-179009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:178996400-179000800	Enhancers	Primary T cells from cord blood	blood
5	chr1:178996400-179001400	Weak transcription	Aorta	Aorta
6	chr1:178996400-179001800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:178996400-179003200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:178996400-179003200	Weak transcription	Esophagus	oesophagus
9	chr1:178996400-179006200	Weak transcription	Fetal Stomach	stomach
10	chr1:178996400-179011200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:178996600-179001000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:178996600-179004000	Weak transcription	Fetal Kidney	kidney
13	chr1:178996800-179000600	Enhancers	Liver	Liver
14	chr1:178996800-179000600	Weak transcription	Fetal Lung	lung
15	chr1:178996800-179000600	Weak transcription	HSMMtube	muscle
16	chr1:178996800-179000800	Weak transcription	Fetal Brain Female	brain
17	chr1:178996800-179001000	Weak transcription	NH-A	brain
18	chr1:178996800-179001400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:178996800-179001400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:178996800-179001800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:178996800-179002600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:178996800-179003000	Weak transcription	Right Ventricle	heart
23	chr1:178996800-179003200	Weak transcription	Thymus	Thymus
24	chr1:178997000-179000800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:178997000-179000800	Weak transcription	HSMM	muscle
26	chr1:178997000-179000800	Weak transcription	Osteobl	bone
27	chr1:178997000-179001000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:178997000-179001000	Weak transcription	HMEC	breast
29	chr1:178997000-179001400	Weak transcription	HUVEC	blood vessel
30	chr1:178997000-179003200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:178997000-179003200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:178997000-179005800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:178997200-179000200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:178997200-179003200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:178997400-179000200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:178997600-179002200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:178997600-179002200	Flanking Active TSS	GM12878-XiMat	blood
38	chr1:178997800-179000600	Flanking Active TSS	K562	blood
39	chr1:178997800-179001400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:178997800-179001800	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:178997800-179004800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:178998200-179000200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:178998200-179000800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:178998200-179001600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:178998200-179002000	Enhancers	Adipose Nuclei	Adipose
46	chr1:178998200-179002200	Enhancers	NHEK	skin
47	chr1:178998200-179002400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:178998200-179002400	Enhancers	Fetal Heart	heart
49	chr1:178998200-179002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:178998200-179004800	Enhancers	Skeletal Muscle Male	skeletal muscle

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