Variant report

Variant	rs4314890
Chromosome Location	chr1:94224412-94224413
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94221637..94224412-chr1:94243135..94245798,2	MCF-7	breast:
2	chr1:94223826..94225778-chr1:94232958..94235783,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10489604	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10782966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782967	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165020	0.89[EUR][1000 genomes]
rs11165022	0.83[JPT][hapmap]
rs11165024	0.87[EUR][1000 genomes]
rs11165026	0.83[JPT][hapmap]
rs12027630	0.85[EUR][1000 genomes]
rs12041975	0.83[JPT][hapmap]
rs12122113	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12123957	0.83[EUR][1000 genomes]
rs12134359	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12137687	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140446	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12143274	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12143279	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12563731	0.87[EUR][1000 genomes]
rs12565614	0.88[EUR][1000 genomes]
rs12566531	0.87[EUR][1000 genomes]
rs12734571	0.85[EUR][1000 genomes]
rs12739186	0.89[EUR][1000 genomes]
rs12745990	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398798	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884018	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs1980083	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2143990	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143992	0.83[JPT][hapmap]
rs2235971	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs2391315	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs2747039	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747041	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747043	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2747045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747050	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2818160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818162	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818164	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818169	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3000471	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3747965	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4075523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141736	0.85[EUR][1000 genomes]
rs4141737	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs4240955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350209	0.83[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4847255	0.81[EUR][1000 genomes]
rs4847256	0.85[CEU][hapmap]
rs4847264	0.83[JPT][hapmap]
rs6663218	0.82[JPT][hapmap]
rs6664719	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs6681265	0.82[JPT][hapmap]
rs6685747	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7364910	0.88[EUR][1000 genomes]
rs743111	0.82[JPT][hapmap]
rs8179391	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871854	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4314890	RP11-488P3.1	cis	Artery Tibial	GTEx
rs4314890	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4314890	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs4314890	RP11-488P3.1	cis	Thyroid	GTEx
rs4314890	RP11-488P3.1	cis	lung	GTEx
rs4314890	RP11-488P3.1	cis	Stomach	GTEx
rs4314890	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs4314890	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs4314890	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs4314890	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94216000-94224800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:94218800-94225200	Enhancers	NHLF	lung
3	chr1:94219800-94224800	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:94219800-94226200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:94219800-94231600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:94220000-94224800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:94220000-94254200	Weak transcription	Aorta	Aorta
8	chr1:94221200-94225600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:94221200-94225600	Enhancers	Fetal Lung	lung
10	chr1:94221200-94226600	Enhancers	Placenta	Placenta
11	chr1:94221400-94225600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:94221400-94225600	Genic enhancers	HMEC	breast
13	chr1:94222200-94225000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:94222400-94225000	Enhancers	Fetal Muscle Leg	muscle
15	chr1:94222400-94225600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:94222400-94225800	Enhancers	Adipose Nuclei	Adipose
17	chr1:94222400-94228200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:94222600-94225200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:94222600-94225600	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:94222600-94225600	Enhancers	Lung	lung
21	chr1:94222800-94224600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:94222800-94224800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:94222800-94225000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:94223000-94224800	Weak transcription	Psoas Muscle	Psoas
25	chr1:94223000-94237000	Weak transcription	NHEK	skin
26	chr1:94223400-94226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:94223600-94224600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:94223600-94225400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:94223600-94225600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr1:94223600-94229200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:94223800-94224600	Flanking Active TSS	Hela-S3	cervix
32	chr1:94223800-94225400	Enhancers	Thymus	Thymus
33	chr1:94223800-94225600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:94223800-94225600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:94223800-94225600	Enhancers	Fetal Intestine Small	intestine
36	chr1:94223800-94225800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:94224000-94225200	Enhancers	Primary T cells from cord blood	blood
38	chr1:94224000-94225200	Flanking Active TSS	HepG2	liver
39	chr1:94224200-94224600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:94224200-94224600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:94224200-94224600	Enhancers	Brain Substantia Nigra	brain
42	chr1:94224200-94224600	Active TSS	Fetal Brain Male	brain
43	chr1:94224200-94224800	Enhancers	HSMMtube	muscle
44	chr1:94224200-94225000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:94224200-94225000	Enhancers	Fetal Stomach	stomach
46	chr1:94224200-94225000	Enhancers	NH-A	brain
47	chr1:94224200-94225400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:94224200-94225400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:94224200-94225400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:94224200-94225400	Enhancers	Osteobl	bone

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