Variant report

Variant	rs2540977
Chromosome Location	chr2:37462228-37462229
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr2:37462211-37462688	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37461002..37463569-chr2:37509247..37510932,2	K562	blood:
2	chr2:37460819..37462677-chr2:37478640..37481087,2	K562	blood:
3	chr2:37461691..37463577-chr2:37472190..37474788,2	K562	blood:

Variant related genes	Relation type
CEBPZ	TF binding region
ENSG00000003509	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10048628	1.00[CHB][hapmap]
rs10177970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10178975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10779921	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11124575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12611683	0.85[EUR][1000 genomes]
rs12712530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022403	1.00[JPT][hapmap]
rs13409250	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17332720	1.00[CHB][hapmap]
rs17498637	1.00[CHB][hapmap]
rs17505250	1.00[CHB][hapmap]
rs1861444	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041840	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110962	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2110964	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160391	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2160392	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2160393	0.92[EUR][1000 genomes]
rs2160395	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249965	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300880	1.00[JPT][hapmap]
rs2372888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372990	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430494	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465488	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2540972	0.86[EUR][1000 genomes]
rs2540973	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2540975	1.00[JPT][hapmap]
rs2714470	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770768	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3845783	1.00[JPT][hapmap]
rs3845785	1.00[JPT][hapmap]
rs3902740	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4670193	1.00[JPT][hapmap]
rs4670671	1.00[JPT][hapmap]
rs4670678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670686	1.00[JPT][hapmap]
rs4670687	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4670691	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544065	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544067	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6730503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742641	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7579990	0.94[EUR][1000 genomes]
rs7583355	1.00[JPT][hapmap]
rs7593932	0.80[CEU][hapmap]
rs759461	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7601628	0.96[EUR][1000 genomes]
rs7602924	0.93[EUR][1000 genomes]
rs7605677	1.00[JPT][hapmap]
rs8243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2540977	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37459800-37465000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:37460000-37463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:37460000-37463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:37460000-37468200	Weak transcription	Psoas Muscle	Psoas
5	chr2:37460000-37468600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:37460000-37471200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:37460000-37474000	Weak transcription	Colonic Mucosa	Colon
8	chr2:37460000-37495600	Weak transcription	Small Intestine	intestine
9	chr2:37460000-37501600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:37460200-37462600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:37460200-37463800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:37460200-37464600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:37460200-37464600	Weak transcription	NHLF	lung
14	chr2:37460200-37465200	Weak transcription	Primary B cells from cord blood	blood
15	chr2:37460200-37466600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:37460200-37468400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:37460200-37468800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
19	chr2:37460400-37462400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:37460400-37462400	Weak transcription	HSMM	muscle
21	chr2:37460400-37463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:37460400-37463200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:37460400-37463200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:37460400-37463200	Weak transcription	Fetal Thymus	thymus
25	chr2:37460400-37463200	Weak transcription	A549	lung
26	chr2:37460400-37463400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:37460400-37463400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:37460400-37463600	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:37460400-37464000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:37460400-37464000	Weak transcription	Primary T cells from cord blood	blood
31	chr2:37460400-37464000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:37460400-37464400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:37460400-37464400	Weak transcription	Adipose Nuclei	Adipose
34	chr2:37460400-37464400	Weak transcription	Liver	Liver
35	chr2:37460400-37464400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:37460400-37464400	Weak transcription	Osteobl	bone
37	chr2:37460400-37464600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:37460400-37464600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:37460400-37464600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:37460400-37464600	Weak transcription	Brain Anterior Caudate	brain
41	chr2:37460400-37464600	Weak transcription	Fetal Lung	lung
42	chr2:37460400-37464600	Weak transcription	Placenta	Placenta
43	chr2:37460400-37464600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:37460400-37464600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:37460400-37464800	Weak transcription	Fetal Intestine Large	intestine
46	chr2:37460400-37465200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:37460400-37465200	Weak transcription	Fetal Brain Female	brain
48	chr2:37460400-37465400	Weak transcription	Lung	lung
49	chr2:37460400-37465600	Weak transcription	Left Ventricle	heart
50	chr2:37460400-37465800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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