Variant report

Variant	rs1045290
Chromosome Location	chr1:227178700-227178701
allele	C/T
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	NR2F2	chr1:227177755-227178821	K562	blood:	n/a	n/a
2	REST	chr1:227178130-227178897	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr1:227169948-227179599	K562	blood:	n/a	n/a
4	REST	chr1:227178342-227178794	H1-neurons	neurons:	n/a	n/a
5	TBL1XR1	chr1:227178526-227178803	K562	blood:	n/a	n/a
6	POLR2A	chr1:227178339-227178713	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227127714..227130249-chr1:227177075..227179669,4	K562	blood:
2	chr1:227176748..227179639-chr1:227203696..227206126,2	K562	blood:

Variant related genes	Relation type
ENSG00000233706	TF binding region
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1045252	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1045285	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1045286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045287	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[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]
rs1045289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916075	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11577007	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11578103	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11578479	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11580229	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11586604	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587443	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588904	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11589344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403236	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12406714	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12409230	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12409428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409755	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12410103	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12593	0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1343743	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1343744	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17528667	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17592479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17600627	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17600669	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600725	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1929862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1929863	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1929864	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2104860	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2183836	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297412	0.95[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297415	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2297416	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2297418	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3738725	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[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];0.98[ASN][1000 genomes]
rs3738729	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3768419	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]
rs3768421	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768423	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3768424	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768425	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795445	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3795446	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3795449	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];0.95[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]
rs3795451	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][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];1.00[ASN][1000 genomes]
rs3795453	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61834001	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61834004	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834005	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834006	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426558	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6426559	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659424	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6664955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670924	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6677602	0.92[CEU][hapmap]
rs6684821	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6690803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693535	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6699400	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704144	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68087483	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535826	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7541033	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7549465	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7549586	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552783	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9726097	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9727512	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	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	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1045290	CABC1	cis	parietal	SCAN
rs1045290	ADCK3	cis	Whole Blood	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
3	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:227162400-227181600	Weak transcription	NHEK	skin
6	chr1:227163000-227180000	Weak transcription	HSMM	muscle
7	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
9	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:227174800-227179400	Enhancers	Stomach Mucosa	stomach
11	chr1:227174800-227182000	Weak transcription	NHDF-Ad	bronchial
12	chr1:227175200-227181200	Strong transcription	Fetal Muscle Leg	muscle
13	chr1:227175200-227198400	Weak transcription	A549	lung
14	chr1:227175200-227210200	Weak transcription	HMEC	breast
15	chr1:227175400-227178800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:227175400-227182600	Genic enhancers	Fetal Intestine Small	intestine
17	chr1:227175600-227178800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:227175600-227179000	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:227175600-227179200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:227175600-227180600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:227175600-227181600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:227175600-227182200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:227175800-227179000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:227175800-227180400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:227175800-227181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:227175800-227181800	Enhancers	Fetal Intestine Large	intestine
29	chr1:227176000-227179200	Enhancers	HepG2	liver
30	chr1:227176000-227181800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:227176000-227181800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
33	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:227176000-227216400	Weak transcription	NHLF	lung
35	chr1:227176200-227181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:227176400-227179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:227176400-227180200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:227176400-227180200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:227176400-227190400	Weak transcription	Osteobl	bone
40	chr1:227176600-227178800	Enhancers	Right Atrium	heart
41	chr1:227176600-227179400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:227176600-227181800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:227176600-227182400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:227176800-227180000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:227176800-227180400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:227176800-227181400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:227177000-227181600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227177000-227181600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:227177000-227181800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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