Variant report

Variant	rs4240956
Chromosome Location	chr1:94223769-94223770
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94216403..94218714-chr1:94221933..94224075,2	MCF-7	breast:
2	chr1:94145323..94148892-chr1:94219465..94224318,4	MCF-7	breast:
3	chr1:94221637..94224412-chr1:94243135..94245798,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

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]
rs10489603	0.91[GIH][hapmap]
rs10489604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][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	1.00[CEU][hapmap];0.90[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[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][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]
rs12565817	0.91[GIH][hapmap]
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	0.96[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	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2391315	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][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[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4075523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][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[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][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]
rs4314890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350209	0.86[ASW][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][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[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][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
rs4240956	RP11-488P3.1	cis	Artery Tibial	GTEx
rs4240956	RP11-488P3.1	cis	Thyroid	GTEx
rs4240956	RP11-488P3.1	cis	lung	GTEx
rs4240956	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs4240956	RP11-488P3.1	cis	Stomach	GTEx
rs4240956	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs4240956	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs4240956	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs4240956	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs4240956	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:56 , 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	chr1:94216400-94223800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:94216800-94224400	Weak transcription	Right Atrium	heart
4	chr1:94218000-94223800	Weak transcription	Thymus	Thymus
5	chr1:94218000-94224200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:94218800-94225200	Enhancers	NHLF	lung
7	chr1:94219600-94223800	Weak transcription	Spleen	Spleen
8	chr1:94219600-94224200	Weak transcription	Fetal Thymus	thymus
9	chr1:94219800-94223800	Enhancers	Hela-S3	cervix
10	chr1:94219800-94224800	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:94219800-94226200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:94219800-94231600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:94220000-94224200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:94220000-94224800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:94220000-94254200	Weak transcription	Aorta	Aorta
16	chr1:94220200-94224200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:94220600-94223800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:94220600-94224200	Weak transcription	HSMMtube	muscle
19	chr1:94221200-94225600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:94221200-94225600	Enhancers	Fetal Lung	lung
21	chr1:94221200-94226600	Enhancers	Placenta	Placenta
22	chr1:94221400-94224200	Weak transcription	NH-A	brain
23	chr1:94221400-94225600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:94221400-94225600	Genic enhancers	HMEC	breast
25	chr1:94221600-94224400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:94221800-94223800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:94222200-94224400	Weak transcription	A549	lung
28	chr1:94222200-94225000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:94222400-94224000	Enhancers	HepG2	liver
30	chr1:94222400-94224200	Weak transcription	Fetal Stomach	stomach
31	chr1:94222400-94225000	Enhancers	Fetal Muscle Leg	muscle
32	chr1:94222400-94225600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:94222400-94225800	Enhancers	Adipose Nuclei	Adipose
34	chr1:94222400-94228200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:94222600-94224200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:94222600-94224200	Weak transcription	HSMM	muscle
37	chr1:94222600-94225200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:94222600-94225600	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:94222600-94225600	Enhancers	Lung	lung
40	chr1:94222800-94223800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:94222800-94224400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:94222800-94224600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:94222800-94224800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:94222800-94225000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:94223000-94224200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:94223000-94224200	Weak transcription	Osteobl	bone
47	chr1:94223000-94224800	Weak transcription	Psoas Muscle	Psoas
48	chr1:94223000-94237000	Weak transcription	NHEK	skin
49	chr1:94223400-94226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:94223600-94223800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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