Variant report

Variant	rs1861444
Chromosome Location	chr2:37464511-37464512
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37455061..37456837-chr2:37463008..37464673,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10177970	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10178975	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10779921	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs11124575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs12611683	0.86[EUR][1000 genomes]
rs12712530	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022403	1.00[JPT][hapmap]
rs13409250	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[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]
rs2041837	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041840	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110962	0.92[EUR][1000 genomes]
rs2110964	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160391	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2160392	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2160393	0.91[EUR][1000 genomes]
rs2160395	1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249965	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300880	1.00[JPT][hapmap]
rs2372888	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372990	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430494	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465488	0.84[EUR][1000 genomes]
rs2540972	0.85[EUR][1000 genomes]
rs2540973	0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2540975	1.00[JPT][hapmap]
rs2540977	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714470	0.96[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];0.91[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	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670686	1.00[JPT][hapmap]
rs4670687	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4670691	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544065	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544067	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6730503	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742641	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7579990	0.92[EUR][1000 genomes]
rs7583355	1.00[JPT][hapmap]
rs7593932	0.84[TSI][hapmap]
rs759461	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs7601628	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7602924	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7605677	1.00[JPT][hapmap]
rs8243	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1861444	PRKD3	Cis_1M	lymphoblastoid	RTeQTL
rs1861444	QPCT	cis	parietal	SCAN
rs1861444	QPCT	cis	multi-tissue	Pritchard
rs1861444	CEBPZ	cis	lymphoblastoid	seeQTL
rs1861444	PRKD3	cis	parietal	SCAN
rs1861444	CCDC75	cis	parietal	SCAN

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	chr2:37460000-37468200	Weak transcription	Psoas Muscle	Psoas
3	chr2:37460000-37468600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:37460000-37471200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:37460000-37474000	Weak transcription	Colonic Mucosa	Colon
6	chr2:37460000-37495600	Weak transcription	Small Intestine	intestine
7	chr2:37460000-37501600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:37460200-37464600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:37460200-37464600	Weak transcription	NHLF	lung
10	chr2:37460200-37465200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:37460200-37466600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:37460200-37468400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:37460200-37468800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
15	chr2:37460400-37464600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:37460400-37464600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:37460400-37464600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:37460400-37464600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:37460400-37464600	Weak transcription	Fetal Lung	lung
20	chr2:37460400-37464600	Weak transcription	Placenta	Placenta
21	chr2:37460400-37464600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:37460400-37464600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:37460400-37464800	Weak transcription	Fetal Intestine Large	intestine
24	chr2:37460400-37465200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:37460400-37465200	Weak transcription	Fetal Brain Female	brain
26	chr2:37460400-37465400	Weak transcription	Lung	lung
27	chr2:37460400-37465600	Weak transcription	Left Ventricle	heart
28	chr2:37460400-37465800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:37460400-37466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:37460400-37466200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:37460400-37466200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:37460400-37467200	Weak transcription	Esophagus	oesophagus
33	chr2:37460400-37467200	Weak transcription	Pancreas	Pancrea
34	chr2:37460400-37467400	Weak transcription	NHDF-Ad	bronchial
35	chr2:37460400-37468000	Weak transcription	HUVEC	blood vessel
36	chr2:37460400-37468400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:37460400-37468400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:37460400-37468400	Weak transcription	NH-A	brain
39	chr2:37460400-37468600	Weak transcription	Brain Angular Gyrus	brain
40	chr2:37460400-37468600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:37460400-37468800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:37460400-37468800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:37460400-37469000	Weak transcription	HMEC	breast
44	chr2:37460400-37470600	Weak transcription	Fetal Kidney	kidney
45	chr2:37460400-37471200	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:37460400-37472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:37460400-37472400	Weak transcription	Brain Substantia Nigra	brain
48	chr2:37460400-37476600	Weak transcription	Right Ventricle	heart
49	chr2:37460400-37481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:37460400-37492200	Weak transcription	Fetal Heart	heart

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