Variant report

Variant	rs3766709
Chromosome Location	chr1:186295930-186295931
allele	A/G
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	IRF1	chr1:186295916-186296000	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186295688..186297629-chr1:186322768..186325332,2	MCF-7	breast:

Variant related genes	Relation type
TPR	TF binding region
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494586	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10911855	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16825295	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs1919198	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2026187	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2037830	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141393	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2178215	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2383476	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3115761	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3124814	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131550	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3131551	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3131558	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3766706	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766708	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425026	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657726	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700930	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7756	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878041	0.83[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8824	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3394491	chr1:186295429-186297527	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv1847807	chr1:186295930-186339878	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv548399	chr1:186295930-186353461	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3766709	OCLM	cis	parietal	SCAN
rs3766709	C1orf27	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186272000-186306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:186277600-186342600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:186277800-186297000	Strong transcription	Primary B cells from cord blood	blood
4	chr1:186278400-186342600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:186278800-186320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:186279400-186342400	Strong transcription	Fetal Thymus	thymus
7	chr1:186279600-186317600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:186279600-186342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:186280000-186317600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:186280000-186320200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:186280000-186340400	Strong transcription	Dnd41	blood
12	chr1:186280000-186342000	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:186280000-186342400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:186280000-186342400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:186280000-186342400	Strong transcription	Osteobl	bone
16	chr1:186280000-186342600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:186280000-186342600	Strong transcription	HSMM	muscle
18	chr1:186280200-186297200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr1:186280200-186316800	Strong transcription	Placenta	Placenta
20	chr1:186280200-186342200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:186280400-186317600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:186280400-186317600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:186280400-186342400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:186280800-186342600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:186281000-186341800	Strong transcription	Liver	Liver
26	chr1:186281000-186342600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:186281200-186297400	Strong transcription	NHDF-Ad	bronchial
28	chr1:186281200-186297600	Strong transcription	Fetal Intestine Large	intestine
29	chr1:186281200-186317600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:186281200-186317800	Strong transcription	HUVEC	blood vessel
31	chr1:186281200-186338200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr1:186281200-186341400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:186281200-186341800	Strong transcription	Adipose Nuclei	Adipose
34	chr1:186281200-186342200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:186281200-186342200	Strong transcription	NH-A	brain
36	chr1:186281400-186297600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:186281400-186341600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:186281400-186342000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:186281400-186342000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:186281400-186342000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:186281400-186342200	Strong transcription	Hela-S3	cervix
42	chr1:186281400-186342400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:186281400-186342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:186281600-186297200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:186281800-186335600	Strong transcription	HMEC	breast
46	chr1:186281800-186342200	Strong transcription	K562	blood
47	chr1:186282400-186319600	Weak transcription	Stomach Mucosa	stomach
48	chr1:186283400-186341000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:186283800-186297000	Strong transcription	Primary hematopoietic stem cells	blood
50	chr1:186283800-186327800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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