Variant report

Variant	rs2540973
Chromosome Location	chr2:37428743-37428744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37422648..37425855-chr2:37426588..37429472,6	MCF-7	breast:
2	chr2:37416656..37421292-chr2:37425395..37428971,5	MCF-7	breast:
3	chr2:37426617..37429540-chr2:37457354..37459837,4	MCF-7	breast:
4	chr2:37427347..37429134-chr2:37454276..37457065,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115816	Chromatin interaction
ENSG00000138068	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000218739	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10177970	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs10178975	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10779921	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11124575	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12712530	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13022403	1.00[JPT][hapmap]
rs13409250	0.85[EUR][1000 genomes]
rs13410628	1.00[JPT][hapmap]
rs1861444	0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2041837	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2041840	0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2110962	0.82[EUR][1000 genomes]
rs2110964	0.87[EUR][1000 genomes]
rs2160391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160392	0.81[EUR][1000 genomes]
rs2160393	0.81[EUR][1000 genomes]
rs2160395	0.87[EUR][1000 genomes]
rs2249965	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2300880	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2372888	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2372990	0.80[EUR][1000 genomes]
rs2430494	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2465488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2540972	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2540974	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2540975	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2540977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2714470	0.86[EUR][1000 genomes]
rs3770768	1.00[JPT][hapmap]
rs3845783	1.00[JPT][hapmap]
rs3845785	1.00[JPT][hapmap]
rs3902740	0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs4648186	1.00[JPT][hapmap]
rs4670193	1.00[JPT][hapmap]
rs4670671	1.00[JPT][hapmap]
rs4670678	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4670686	1.00[JPT][hapmap]
rs4670687	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs6544065	0.82[EUR][1000 genomes]
rs6544067	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs6730503	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7579990	0.81[EUR][1000 genomes]
rs7583355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7593932	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs759461	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7601628	0.84[EUR][1000 genomes]
rs7602924	0.82[EUR][1000 genomes]
rs7605677	1.00[JPT][hapmap]
rs8243	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2540973	QPCT	cis	parietal	SCAN
rs2540973	PRKD3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37424400-37430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:37424400-37433200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:37424400-37446400	Weak transcription	Small Intestine	intestine
4	chr2:37424600-37429000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:37424600-37430400	Weak transcription	Fetal Heart	heart
6	chr2:37424600-37430600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:37424600-37430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:37424600-37430800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:37424600-37430800	Weak transcription	Brain Angular Gyrus	brain
10	chr2:37424600-37430800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:37424600-37430800	Weak transcription	Gastric	stomach
12	chr2:37424800-37429000	Weak transcription	Primary T cells from cord blood	blood
13	chr2:37424800-37429000	Weak transcription	Aorta	Aorta
14	chr2:37424800-37430600	Weak transcription	Brain Substantia Nigra	brain
15	chr2:37424800-37430800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:37424800-37430800	Weak transcription	Thymus	Thymus
17	chr2:37424800-37430800	Weak transcription	HSMMtube	muscle
18	chr2:37424800-37433200	Weak transcription	Right Atrium	heart
19	chr2:37425000-37429000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:37425000-37429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:37425000-37433200	Weak transcription	Esophagus	oesophagus
22	chr2:37425000-37433200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:37425000-37444200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:37425200-37429000	Weak transcription	Left Ventricle	heart
25	chr2:37425200-37430600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:37425200-37430800	Weak transcription	Right Ventricle	heart
27	chr2:37425200-37433000	Weak transcription	Colonic Mucosa	Colon
28	chr2:37425200-37433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:37425200-37433200	Weak transcription	Pancreas	Pancrea
30	chr2:37425200-37433200	Weak transcription	Stomach Mucosa	stomach
31	chr2:37425200-37433200	Weak transcription	Spleen	Spleen
32	chr2:37425800-37429400	Genic enhancers	Dnd41	blood
33	chr2:37425800-37430600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:37426000-37429800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:37426000-37430400	Weak transcription	K562	blood
36	chr2:37426200-37430800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:37426200-37438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:37426400-37429400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
39	chr2:37426600-37430400	Strong transcription	A549	lung
40	chr2:37426600-37433600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:37426600-37438200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:37426600-37451400	Strong transcription	Fetal Thymus	thymus
43	chr2:37426800-37429000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:37426800-37429000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:37426800-37429000	Strong transcription	GM12878-XiMat	blood
46	chr2:37426800-37430600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:37426800-37430600	Strong transcription	Fetal Lung	lung
48	chr2:37426800-37433200	Strong transcription	Primary B cells from cord blood	blood
49	chr2:37427000-37429000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:37427000-37429200	Strong transcription	Fetal Brain Female	brain

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