Variant report

Variant	rs1903009
Chromosome Location	chr4:89856277-89856278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89853119..89856686-chr4:89857478..89862427,5	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10001420	0.83[ASN][1000 genomes]
rs10019862	0.96[ASN][1000 genomes]
rs10028121	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs10033435	0.92[ASN][1000 genomes]
rs10033476	0.92[ASN][1000 genomes]
rs1246630	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246633	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246635	0.81[EUR][1000 genomes]
rs1246637	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246638	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246639	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1246641	1.00[ASN][1000 genomes]
rs1272570	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13106968	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13148439	0.96[ASN][1000 genomes]
rs1379934	1.00[CHB][hapmap]
rs1398938	0.83[ASN][1000 genomes]
rs1398939	0.83[ASN][1000 genomes]
rs1398941	0.83[ASN][1000 genomes]
rs1458552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458555	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533294	1.00[CHB][hapmap]
rs1795730	0.83[ASN][1000 genomes]
rs1795737	0.83[ASN][1000 genomes]
rs1795740	0.83[ASN][1000 genomes]
rs1903004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2045516	1.00[ASN][1000 genomes]
rs2125410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446295	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446302	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2446309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464511	0.83[ASN][1000 genomes]
rs2464521	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2609254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2609274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2609278	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609281	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609284	0.92[ASN][1000 genomes]
rs2670619	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2670620	0.83[ASN][1000 genomes]
rs2704572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704591	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704602	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704603	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704606	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28559811	0.83[ASN][1000 genomes]
rs28624770	0.96[ASN][1000 genomes]
rs28658282	0.96[ASN][1000 genomes]
rs2869965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869968	1.00[ASN][1000 genomes]
rs28869547	0.83[ASN][1000 genomes]
rs4498109	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59698155	0.96[ASN][1000 genomes]
rs7673427	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697878	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs922027	1.00[ASW][hapmap];0.95[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]
rs973680	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs987314	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs993358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999793	0.83[ASN][1000 genomes]
rs9999873	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv879533	chr4:89832532-89917135	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv1829430	chr4:89853598-89908308	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1903009	ABCG2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89820000-89859200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:89825600-89878400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:89840800-89862800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:89845400-89859600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:89845400-89866400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:89845600-89857600	Weak transcription	Gastric	stomach
7	chr4:89847200-89858800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:89847400-89858200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:89848400-89861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:89850200-89878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:89850400-89861200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:89851400-89859200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:89851400-89883600	Weak transcription	Fetal Intestine Large	intestine
14	chr4:89852400-89857400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:89852400-89857600	Weak transcription	Pancreas	Pancrea
16	chr4:89852400-89885000	Weak transcription	Fetal Lung	lung
17	chr4:89852600-89865400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:89852600-89877800	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:89852600-89879200	Weak transcription	Fetal Stomach	stomach
20	chr4:89852600-89879400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:89853200-89857600	Active TSS	Placenta	Placenta
22	chr4:89853600-89859000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:89854400-89860200	Weak transcription	Fetal Heart	heart
24	chr4:89854800-89865200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:89855000-89857400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:89855000-89858600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:89855000-89860200	Weak transcription	Primary T cells from cord blood	blood
28	chr4:89855000-89860200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:89855000-89860600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:89855200-89860200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:89855200-89860200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:89855400-89859400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:89855400-89860200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:89855600-89858400	Weak transcription	Fetal Intestine Small	intestine
35	chr4:89855800-89863200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:89856000-89856400	ZNF genes & repeats	Aorta	Aorta
37	chr4:89856000-89856400	Enhancers	Spleen	Spleen
38	chr4:89856000-89857800	Strong transcription	Ovary	ovary
39	chr4:89856200-89857400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:89856200-89857800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:89856200-89858400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:89856200-89861000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:89856200-89869200	Weak transcription	Left Ventricle	heart

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