Variant report

Variant	rs3766089
Chromosome Location	chr1:169268812-169268813
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	chr1:169265989..169270734-chr1:169271559..169276402,6	K562	blood:
2	chr1:169267146..169270567-chr1:169272063..169277859,6	K562	blood:

Variant related genes	Relation type
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10158265	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10158861	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800439	0.86[CHB][hapmap]
rs10800441	0.86[CHB][hapmap]
rs10919088	0.91[AMR][1000 genomes]
rs10919102	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919140	0.81[CEU][hapmap]
rs10919146	1.00[ASN][1000 genomes]
rs11800843	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[YRI][hapmap]
rs11808274	0.81[ASW][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11809378	0.90[ASN][1000 genomes]
rs12023291	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12024897	0.86[CHB][hapmap]
rs12025233	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026996	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030320	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12032783	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033078	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033253	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12035804	0.80[AFR][1000 genomes]
rs12036968	0.91[YRI][hapmap]
rs12037211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12043489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043545	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045202	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs12046139	0.82[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047231	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400838	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs1415928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16828170	0.81[ASW][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs16862172	0.90[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[YRI][hapmap]
rs16862199	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap]
rs1980198	0.86[CHB][hapmap]
rs2235195	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[YRI][hapmap]
rs2268048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275299	0.86[CHB][hapmap]
rs34710865	0.92[ASN][1000 genomes]
rs3737682	0.85[CHB][hapmap]
rs3818844	0.86[CHB][hapmap]
rs3820058	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656670	0.86[CHB][hapmap]
rs56341747	0.91[AMR][1000 genomes]
rs58585501	0.80[AMR][1000 genomes]
rs61806986	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808865	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808914	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808915	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664272	0.80[AMR][1000 genomes]
rs6669741	0.85[CHB][hapmap]
rs6677410	0.86[CHB][hapmap]
rs6685556	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696810	0.86[CHB][hapmap]
rs6698149	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7521338	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534737	0.86[CHB][hapmap]
rs7539415	0.86[CHB][hapmap]
rs9633334	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9804101	0.92[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9988595	0.85[AMR][1000 genomes]
rs9988604	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1004674	chr1:169233962-169271792	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3766089	FMO9P	cis	parietal	SCAN
rs3766089	SCYL3	cis	parietal	SCAN
rs3766089	C1orf114	cis	parietal	SCAN
rs3766089	C1orf114	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
6	chr1:169254000-169274800	Weak transcription	Ovary	ovary
7	chr1:169254800-169281000	Weak transcription	Dnd41	blood
8	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
9	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:169258600-169271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:169258600-169276400	Weak transcription	HSMM	muscle
14	chr1:169258800-169274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:169259200-169278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:169259400-169274800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:169259400-169278600	Weak transcription	Adipose Nuclei	Adipose
19	chr1:169259600-169278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
21	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
22	chr1:169260600-169278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:169262400-169271400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:169262800-169274600	Weak transcription	Liver	Liver
25	chr1:169262800-169278600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:169263000-169278600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:169264000-169281400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:169264200-169269800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:169264200-169278600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:169264400-169271600	Weak transcription	Psoas Muscle	Psoas
31	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
32	chr1:169265000-169278600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
34	chr1:169265200-169272800	Weak transcription	HepG2	liver
35	chr1:169265200-169277200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:169265200-169278400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:169265200-169281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:169265400-169281200	Weak transcription	NHDF-Ad	bronchial
39	chr1:169265800-169281000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:169266200-169278600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:169266200-169280200	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:169266600-169269400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:169266800-169269400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:169267000-169278400	Weak transcription	Brain Anterior Caudate	brain
45	chr1:169267000-169281200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:169267800-169269400	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:169267800-169271400	Weak transcription	Primary T cells from cord blood	blood
48	chr1:169267800-169281200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:169268000-169278600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:169268200-169269400	Enhancers	HUVEC	blood vessel

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