Variant report

Variant	rs2372888
Chromosome Location	chr2:37460234-37460235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr2:37460146-37460396	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:37457736-37460395	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:37457149..37460328-chr2:37469330..37472927,4	MCF-7	breast:
2	chr2:37458143..37460778-chr2:37473170..37474857,2	MCF-7	breast:
3	chr2:37458068..37462101-chr2:37468406..37471417,5	K562	blood:
4	chr2:37420975..37425403-chr2:37457376..37460314,8	K562	blood:
5	chr2:37413518..37417531-chr2:37457528..37460316,5	MCF-7	breast:
6	chr2:37456368..37460350-chr2:37466636..37472512,8	MCF-7	breast:

No data

Variant related genes	Relation type
CEBPZ	TF binding region
ENSG00000218739	Chromatin interaction
ENSG00000233159	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000138068	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

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];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10178975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[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];0.91[EUR][1000 genomes]
rs12611683	0.83[EUR][1000 genomes]
rs12712530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022403	1.00[JPT][hapmap]
rs13409250	0.95[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]
rs1861444	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]
rs2041837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041840	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110962	0.91[EUR][1000 genomes]
rs2110964	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160391	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2160392	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2160393	0.90[EUR][1000 genomes]
rs2160395	1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249965	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300880	1.00[JPT][hapmap]
rs2372990	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430494	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465488	0.86[EUR][1000 genomes]
rs2540972	0.87[EUR][1000 genomes]
rs2540973	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2540975	1.00[JPT][hapmap]
rs2540977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714470	0.95[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];0.90[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];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670686	1.00[JPT][hapmap]
rs4670687	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4670691	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544065	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544067	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6730503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742641	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7579990	0.92[EUR][1000 genomes]
rs7583355	1.00[JPT][hapmap]
rs7593932	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs759461	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs7601628	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7602924	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7605677	1.00[JPT][hapmap]
rs8243	1.00[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
rs2372888	CCDC75	cis	parietal	SCAN
rs2372888	PRKD3	cis	Liver	GTEx
rs2372888	QPCT	cis	multi-tissue	Pritchard
rs2372888	QPCT	cis	parietal	SCAN
rs2372888	PRKD3	cis	multi-tissue	Pritchard
rs2372888	PRKD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37456600-37460400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:37456800-37460600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:37457000-37461000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr2:37457200-37460400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:37457200-37461000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:37457600-37460400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:37459200-37460400	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr2:37459400-37460400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr2:37459400-37460400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr2:37459400-37460400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr2:37459400-37460400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:37459400-37460400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:37459400-37460400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr2:37459400-37460400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr2:37459400-37460400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr2:37459400-37460400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr2:37459400-37460400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr2:37459400-37460400	Flanking Active TSS	Dnd41	blood
19	chr2:37459400-37460400	Flanking Active TSS	Hela-S3	cervix
20	chr2:37459400-37460400	Flanking Active TSS	NHEK	skin
21	chr2:37459600-37460400	Enhancers	Gastric	stomach
22	chr2:37459600-37460400	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr2:37459600-37460600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr2:37459600-37460600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:37459800-37460400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:37459800-37460400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr2:37459800-37460400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:37459800-37460400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:37459800-37460400	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:37459800-37460400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:37459800-37460400	Enhancers	Liver	Liver
32	chr2:37459800-37460400	Enhancers	Esophagus	oesophagus
33	chr2:37459800-37460400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:37459800-37460400	Enhancers	Fetal Heart	heart
35	chr2:37459800-37460400	Enhancers	Fetal Intestine Large	intestine
36	chr2:37459800-37460400	Enhancers	Fetal Muscle Leg	muscle
37	chr2:37459800-37460400	Enhancers	Placenta	Placenta
38	chr2:37459800-37460400	Enhancers	Fetal Thymus	thymus
39	chr2:37459800-37460400	Enhancers	Left Ventricle	heart
40	chr2:37459800-37460400	Enhancers	Lung	lung
41	chr2:37459800-37460400	Enhancers	Pancreas	Pancrea
42	chr2:37459800-37460400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:37459800-37460400	Enhancers	Thymus	Thymus
44	chr2:37459800-37460600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:37459800-37460600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:37459800-37460600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:37459800-37460600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:37459800-37460600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:37459800-37460600	Enhancers	Ovary	ovary
50	chr2:37459800-37460600	Enhancers	Spleen	Spleen

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