Variant report

Variant	rs3768419
Chromosome Location	chr1:227173477-227173478
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	chr1:227165601..227167978-chr1:227173311..227176266,3	MCF-7	breast:
2	chr1:227168074..227172579-chr1:227173053..227177156,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1045252	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs1045285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045286	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1045287	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045289	0.81[ASW][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1045290	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10495273	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10495274	0.82[MKK][hapmap]
rs10916075	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577007	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11578103	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11578479	0.91[ASN][1000 genomes]
rs11580229	0.91[ASN][1000 genomes]
rs11583229	0.89[ASN][1000 genomes]
rs11583489	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11586604	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11587443	0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11588904	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11589344	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1186	0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12403236	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12403775	0.90[CHB][hapmap]
rs12405857	0.89[ASN][1000 genomes]
rs12406714	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12409230	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12409428	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12409755	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12410103	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12593	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1319103	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1343743	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343744	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1343745	0.96[ASN][1000 genomes]
rs17528667	0.83[AMR][1000 genomes]
rs17592479	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17600627	0.82[AMR][1000 genomes]
rs17600669	0.83[AMR][1000 genomes]
rs17600725	0.91[ASN][1000 genomes]
rs17600747	0.89[ASN][1000 genomes]
rs17600947	0.89[ASN][1000 genomes]
rs1929855	0.93[CHB][hapmap]
rs1929862	0.85[AMR][1000 genomes]
rs1929863	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1929864	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2104860	0.91[ASN][1000 genomes]
rs2183836	0.85[AFR][1000 genomes]
rs2297415	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297416	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297418	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297419	0.96[ASN][1000 genomes]
rs3738725	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3738729	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3768420	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3768421	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768423	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768424	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768425	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3795445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795449	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795451	0.87[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3795453	0.91[ASN][1000 genomes]
rs4146588	0.93[CHB][hapmap]
rs61834001	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61834004	0.83[AMR][1000 genomes]
rs61834006	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61834039	0.89[ASN][1000 genomes]
rs6426558	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6426559	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6426560	0.89[ASN][1000 genomes]
rs6659424	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6664955	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670924	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6677602	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6684821	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6690803	0.81[ASW][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6693535	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6699400	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6704144	0.83[AMR][1000 genomes]
rs68087483	0.83[AMR][1000 genomes]
rs7520272	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7535826	0.91[ASN][1000 genomes]
rs7541033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549465	0.87[ASN][1000 genomes]
rs7549586	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7552783	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7553837	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7555621	0.85[ASN][1000 genomes]
rs9726097	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9727512	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3768419	SERPINA7	trans	cerebellum	SCAN
rs3768419	ADCK3	cis	Whole Blood	GTEx
rs3768419	CDC42BPA	cis	Artery Tibial	GTEx
rs3768419	CABC1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
4	chr1:227154800-227176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:227158400-227174600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:227159000-227175800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:227159800-227174000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:227160000-227173600	Weak transcription	A549	lung
10	chr1:227160000-227174400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:227160000-227174400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:227160000-227174800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:227160000-227177200	Weak transcription	GM12878-XiMat	blood
14	chr1:227160600-227175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:227162200-227176000	Strong transcription	Primary T cells from cord blood	blood
17	chr1:227162400-227173600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:227162400-227174200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:227162400-227174200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:227162400-227175200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:227162400-227181600	Weak transcription	NHEK	skin
22	chr1:227162600-227174200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:227162600-227174200	Weak transcription	Aorta	Aorta
24	chr1:227162600-227175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:227162600-227176600	Strong transcription	Thymus	Thymus
26	chr1:227162800-227173600	Weak transcription	NHLF	lung
27	chr1:227162800-227174000	Weak transcription	Osteobl	bone
28	chr1:227162800-227174200	Weak transcription	NHDF-Ad	bronchial
29	chr1:227163000-227173600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:227163000-227174200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:227163000-227180000	Weak transcription	HSMM	muscle
32	chr1:227163200-227174000	Weak transcription	Small Intestine	intestine
33	chr1:227163200-227175400	Strong transcription	Fetal Intestine Small	intestine
34	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:227163800-227176200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
37	chr1:227164200-227175800	Strong transcription	HepG2	liver
38	chr1:227164400-227174200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:227164400-227175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:227164600-227174200	Strong transcription	Colonic Mucosa	Colon
41	chr1:227164600-227175000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:227164800-227173600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:227164800-227173800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:227164800-227175200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:227165000-227175000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:227165000-227175400	Genic enhancers	Right Ventricle	heart
47	chr1:227165000-227176000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:227165200-227175000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:227165400-227173800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr1:227165400-227175800	Strong transcription	Ovary	ovary

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