Variant report

Variant	rs3770754
Chromosome Location	chr2:37575381-37575382
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37573383..37576359-chr2:37576591..37578098,2	K562	blood:
2	chr2:37573509..37575748-chr2:37602573..37605323,2	MCF-7	breast:
3	chr2:37574642..37576209-chr2:37580099..37581679,2	K562	blood:
4	chr2:37571184..37574506-chr2:37575236..37577117,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115828	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10184179	1.00[LWK][hapmap];0.96[MKK][hapmap]
rs10190959	0.80[CEU][hapmap]
rs10490448	1.00[LWK][hapmap]
rs1056021	0.82[JPT][hapmap]
rs11124569	0.82[JPT][hapmap]
rs1158218	0.80[CEU][hapmap]
rs1158219	0.80[CEU][hapmap]
rs12618410	0.82[JPT][hapmap]
rs17020624	1.00[LWK][hapmap]
rs2041836	0.80[CEU][hapmap]
rs2373000	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2888434	0.86[JPT][hapmap]
rs3770752	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.86[AMR][1000 genomes]
rs4998429	0.86[JPT][hapmap]
rs6734118	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6743782	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv2685	chr2:37550096-37594923	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3770754	QPCT	cis	parietal	SCAN
rs3770754	CEBPZ	cis	cerebellum	SCAN
rs3770754	CEBPZ	cis	lymphoblastoid	seeQTL
rs3770754	CEBPZ	Cis_1M	lymphoblastoid	RTeQTL
rs3770754	PRKD3	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37572400-37576000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:37572400-37576200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37572400-37576600	Weak transcription	Spleen	Spleen
4	chr2:37572600-37575600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:37572600-37575800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:37572600-37575800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:37572600-37576600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:37572600-37576600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:37572600-37576600	Weak transcription	Fetal Kidney	kidney
10	chr2:37572600-37576600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:37572600-37576800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:37572600-37576800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:37572600-37577200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:37572600-37577200	Weak transcription	Liver	Liver
15	chr2:37572600-37577200	Weak transcription	Fetal Intestine Large	intestine
16	chr2:37572600-37577200	Weak transcription	Left Ventricle	heart
17	chr2:37572600-37595400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:37572800-37576000	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:37572800-37576000	Weak transcription	A549	lung
20	chr2:37572800-37576000	Weak transcription	NHDF-Ad	bronchial
21	chr2:37572800-37576200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:37572800-37576800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:37572800-37576800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:37572800-37577200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:37572800-37577200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:37572800-37577200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:37572800-37577200	Weak transcription	Right Atrium	heart
28	chr2:37572800-37577200	Weak transcription	HMEC	breast
29	chr2:37572800-37577200	Weak transcription	Osteobl	bone
30	chr2:37572800-37577600	Weak transcription	NHEK	skin
31	chr2:37573200-37577000	Weak transcription	Adipose Nuclei	Adipose
32	chr2:37573400-37576000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:37573400-37576400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:37573400-37576600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:37573400-37577600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:37573600-37575600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:37573600-37578800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:37574200-37575400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr2:37574200-37576000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr2:37574800-37575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:37575000-37575800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:37575000-37575800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:37575000-37578600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:37575200-37575400	Bivalent Enhancer	Primary B cells from cord blood	blood
45	chr2:37575200-37575400	Enhancers	Fetal Brain Male	brain
46	chr2:37575200-37575400	Bivalent Enhancer	Fetal Lung	lung
47	chr2:37575200-37575800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:37575200-37576200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:37575200-37577000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:37575200-37577400	Enhancers	HUES48 Cell Line	embryonic stem cell

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