Variant report

Variant	rs4743981
Chromosome Location	chr9:97812002-97812003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97765581..97769970-chr9:97809027..97814302,8	MCF-7	breast:
2	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
3	chr9:97679968..97683217-chr9:97810510..97812408,3	MCF-7	breast:
4	chr9:97519868..97522673-chr9:97811342..97812928,2	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1004373	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10117370	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10119512	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10121760	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10123819	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1020963	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10512253	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10761364	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10761366	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10761368	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761369	0.82[EUR][1000 genomes]
rs10761372	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10993427	0.86[AMR][1000 genomes]
rs10993464	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10993467	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1113102	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1412488	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1564234	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1571894	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1571895	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061800	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2404305	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2404456	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3802454	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3802456	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3858089	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4537362	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743979	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743980	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743982	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744422	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4744423	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4744424	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744425	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744426	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744428	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744430	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744431	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744432	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744433	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744435	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744436	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479588	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6479591	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6479592	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7020709	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7021351	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022452	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7043705	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7048786	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7048941	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7851173	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7854831	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7857679	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7862156	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7863291	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7865144	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7871218	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7873479	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7873567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962229	0.88[AMR][1000 genomes];0.90[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	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
5	esv3344238	chr9:97811963-97812232	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743981	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 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	chr9:97810200-97812800	Active TSS	Psoas Muscle	Psoas
4	chr9:97810200-97813000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:97810200-97813000	Active TSS	Aorta	Aorta
6	chr9:97810200-97814000	Active TSS	Stomach Smooth Muscle	stomach
7	chr9:97810400-97812200	Active TSS	Fetal Kidney	kidney
8	chr9:97810400-97812400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr9:97810400-97812800	Active TSS	Right Atrium	heart
10	chr9:97810400-97813000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:97810400-97813000	Active TSS	Colon Smooth Muscle	Colon
12	chr9:97810400-97813000	Active TSS	Ovary	ovary
13	chr9:97810400-97813200	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr9:97810600-97812200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:97810600-97812200	Active TSS	Fetal Stomach	stomach
16	chr9:97810600-97812600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:97810600-97812800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:97810600-97813000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr9:97810800-97812200	Active TSS	NHEK	skin
20	chr9:97810800-97812400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:97810800-97812400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:97810800-97812800	Flanking Active TSS	HepG2	liver
23	chr9:97810800-97813200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:97810800-97813400	Active TSS	NHLF	lung
25	chr9:97810800-97813800	Active TSS	Esophagus	oesophagus
26	chr9:97811000-97812200	Active TSS	HSMMtube	muscle
27	chr9:97811000-97812400	Active TSS	Stomach Mucosa	stomach
28	chr9:97811000-97813200	Transcr. at gene 5' and 3'	Osteobl	bone
29	chr9:97811000-97813400	Active TSS	HMEC	breast
30	chr9:97811200-97812800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:97811200-97813000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:97811200-97815200	Weak transcription	Small Intestine	intestine
33	chr9:97811400-97812200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:97811400-97812200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:97811400-97812200	Active TSS	Fetal Muscle Leg	muscle
36	chr9:97811400-97812200	Weak transcription	Pancreas	Pancrea
37	chr9:97811400-97812400	Weak transcription	Colonic Mucosa	Colon
38	chr9:97811400-97812600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr9:97811400-97812800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:97811400-97812800	Weak transcription	Lung	lung
41	chr9:97811400-97813000	Active TSS	Placenta	Placenta
42	chr9:97811400-97816000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:97811400-97820800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:97811600-97812200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
45	chr9:97811600-97812200	Weak transcription	Left Ventricle	heart
46	chr9:97811600-97812200	Active TSS	K562	blood
47	chr9:97811600-97812400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr9:97811600-97812600	Enhancers	Adipose Nuclei	Adipose
49	chr9:97811600-97812600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:97811600-97812600	Enhancers	HUVEC	blood vessel

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