Variant report

Variant	rs4743984
Chromosome Location	chr9:97813157-97813158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97812899..97815881-chr9:97854427..97857279,2	MCF-7	breast:
2	chr9:97765581..97769970-chr9:97809027..97814302,8	MCF-7	breast:
3	chr9:97812810..97815819-chr9:97816453..97821719,4	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1004373	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117370	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119512	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121760	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512253	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761366	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761368	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761369	0.91[CEU][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10761372	0.80[ASN][1000 genomes]
rs10993427	0.81[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993456	0.82[TSI][hapmap]
rs10993464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12339639	0.82[TSI][hapmap]
rs1412488	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564234	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571895	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404295	0.81[CEU][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs2404302	0.91[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2404305	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404456	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3802456	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858089	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4537362	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743979	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743981	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744422	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744424	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744425	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744426	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744428	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4744431	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744432	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744436	0.82[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479588	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479591	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479592	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020709	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7022452	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043705	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048786	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048941	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851173	0.91[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7854831	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862156	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863291	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865144	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7871218	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873479	0.80[AMR][1000 genomes]
rs7873567	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs962229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4743984	OGN	cis	parietal	SCAN
rs4743984	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL
rs4743984	FOXE1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97809600-97813200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:97810000-97816800	Transcr. at gene 5' and 3'	A549	lung
3	chr9:97810200-97814000	Active TSS	Stomach Smooth Muscle	stomach
4	chr9:97810400-97813200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr9:97810800-97813200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:97810800-97813400	Active TSS	NHLF	lung
7	chr9:97810800-97813800	Active TSS	Esophagus	oesophagus
8	chr9:97811000-97813200	Transcr. at gene 5' and 3'	Osteobl	bone
9	chr9:97811000-97813400	Active TSS	HMEC	breast
10	chr9:97811200-97815200	Weak transcription	Small Intestine	intestine
11	chr9:97811400-97816000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:97811400-97820800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:97811600-97813200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:97811600-97816000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:97811600-97817600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:97811600-97817600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:97811600-97817800	Weak transcription	Right Ventricle	heart
18	chr9:97811800-97813200	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr9:97811800-97815200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:97812000-97813400	Enhancers	Brain Substantia Nigra	brain
21	chr9:97812000-97813400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr9:97812000-97816400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:97812200-97813200	Enhancers	Brain Angular Gyrus	brain
24	chr9:97812400-97813200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:97812400-97814000	Enhancers	Fetal Heart	heart
26	chr9:97812400-97817400	Weak transcription	GM12878-XiMat	blood
27	chr9:97812600-97813200	Active TSS	HSMM	muscle
28	chr9:97812600-97813400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:97812600-97813400	Strong transcription	Liver	Liver
30	chr9:97812600-97813400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:97812600-97813400	Enhancers	Fetal Muscle Leg	muscle
32	chr9:97812600-97813400	Flanking Active TSS	NHEK	skin
33	chr9:97812600-97816400	Weak transcription	HUVEC	blood vessel
34	chr9:97812600-97817400	Weak transcription	Adipose Nuclei	Adipose
35	chr9:97812600-97818600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:97812800-97813200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:97812800-97813200	Enhancers	Brain Cingulate Gyrus	brain
38	chr9:97812800-97813200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr9:97812800-97813400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:97812800-97813400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr9:97812800-97813400	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:97812800-97813400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
43	chr9:97812800-97815200	Enhancers	HepG2	liver
44	chr9:97812800-97816400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:97812800-97816400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:97812800-97816800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:97812800-97817600	Weak transcription	Right Atrium	heart
48	chr9:97813000-97813200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:97813000-97813200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr9:97813000-97813200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin

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