Variant report

Variant	rs1472961
Chromosome Location	chr4:95592144-95592145
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	EP300	chr4:95590594-95592493	A549	lung:	n/a	chr4:95591368-95591378
2	EP300	chr4:95591072-95592177	A549	lung:	n/a	chr4:95591368-95591378
3	GATA3	chr4:95591839-95592261	MCF-7	breast:	n/a	n/a
4	GATA3	chr4:95590773-95592640	A549	lung:	n/a	n/a
5	TCF12	chr4:95589639-95592640	A549	lung:	n/a	n/a
6	POLR2A	chr4:95591974-95592621	A549	lung:	n/a	n/a
7	GATA3	chr4:95591499-95592166	T-47D	breast:	n/a	n/a
8	NR2F2	chr4:95591453-95592222	MCF-7	breast:	n/a	chr4:95591987-95592002
9	FOSL2	chr4:95590473-95592317	A549	lung:	n/a	n/a
10	POLR2A	chr4:95591726-95592929	K562	blood:	n/a	n/a
11	BCL3	chr4:95589771-95592149	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:95585740..95587732-chr4:95591128..95592898,2	MCF-7	breast:
2	chr4:95592122..95594102-chr4:95605165..95607290,2	MCF-7	breast:
3	chr4:95590309..95593538-chr4:95611689..95613963,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249951	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10031423	0.91[EUR][1000 genomes]
rs1043853	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048627	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1056773	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097433	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097434	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097435	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11723532	0.87[EUR][1000 genomes]
rs11724023	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11725850	0.81[EUR][1000 genomes]
rs11732668	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11732687	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs11734014	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12331240	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12331253	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507763	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12511111	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12641023	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12643849	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12643867	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12650641	0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13110828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130496	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472963	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543013	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2280002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2902987	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34403066	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34438564	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34507709	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35959898	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699567	0.89[EUR][1000 genomes]
rs56921499	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60195134	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6532495	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6532496	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6532497	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829381	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6831015	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6839697	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71601224	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7690296	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs951613	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1472961	ATOH1	cis	cerebellum	SCAN
rs1472961	PDLIM5	cis	parietal	SCAN
rs1472961	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
2	chr4:95533800-95594200	Weak transcription	Gastric	stomach
3	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
4	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
6	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
7	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
9	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
10	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:95578600-95593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:95579000-95592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:95582000-95599800	Weak transcription	NHEK	skin
16	chr4:95582400-95592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:95582400-95594200	Weak transcription	Esophagus	oesophagus
18	chr4:95582400-95596200	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:95582400-95598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:95582600-95593800	Weak transcription	Ovary	ovary
21	chr4:95582600-95600000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:95582800-95598000	Weak transcription	Fetal Heart	heart
23	chr4:95585000-95592200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:95585200-95592200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:95585200-95592200	Weak transcription	Adipose Nuclei	Adipose
26	chr4:95585200-95593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:95585200-95598200	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:95586000-95594000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:95586000-95598000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:95586600-95594000	Weak transcription	Fetal Intestine Small	intestine
31	chr4:95586600-95594200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:95587400-95598000	Weak transcription	HSMMtube	muscle
33	chr4:95587600-95592200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:95587600-95592200	Weak transcription	Left Ventricle	heart
35	chr4:95587800-95598400	Weak transcription	HSMM	muscle
36	chr4:95588000-95598400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:95588000-95599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:95588200-95595200	Weak transcription	Placenta	Placenta
39	chr4:95588600-95594200	Weak transcription	Psoas Muscle	Psoas
40	chr4:95589800-95597600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:95589800-95598000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:95590000-95599800	Weak transcription	NH-A	brain
43	chr4:95590200-95592200	Enhancers	HUVEC	blood vessel
44	chr4:95590200-95599800	Weak transcription	HMEC	breast
45	chr4:95590400-95592400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:95590800-95592600	Flanking Active TSS	A549	lung
47	chr4:95590800-95601200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:95591200-95594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:95591400-95593800	Weak transcription	Fetal Kidney	kidney
50	chr4:95591600-95597800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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