Variant report

Variant	rs4743400
Chromosome Location	chr9:98684916-98684917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98665770..98668209-chr9:98683792..98686437,2	K562	blood:
2	chr9:98636162..98639165-chr9:98683503..98686735,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000199202	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10988581	0.82[EUR][1000 genomes]
rs10988792	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988804	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11787559	0.89[AFR][1000 genomes]
rs11790491	0.81[EUR][1000 genomes]
rs11794054	0.82[EUR][1000 genomes]
rs12001	0.93[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683310	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685318	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685807	0.93[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910298	0.81[EUR][1000 genomes]
rs2026032	0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2069053	0.81[EUR][1000 genomes]
rs2274653	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274654	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802438	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743391	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743417	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743418	0.82[EUR][1000 genomes]
rs4743419	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73536517	0.82[EUR][1000 genomes]
rs7868270	0.81[EUR][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	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4743400	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs4743400	LINC00476	cis	Whole Blood	GTEx
rs4743400	LINC00476	cis	Esophagus Muscularis	GTEx
rs4743400	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs4743400	LINC00476	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
3	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:98644400-98685600	Weak transcription	Gastric	stomach
5	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
7	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
9	chr9:98659200-98685600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
11	chr9:98664000-98685600	Weak transcription	Brain Anterior Caudate	brain
12	chr9:98664000-98687400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:98664200-98685200	Weak transcription	Hela-S3	cervix
14	chr9:98664400-98685600	Weak transcription	NHEK	skin
15	chr9:98670800-98687200	Weak transcription	Stomach Mucosa	stomach
16	chr9:98672600-98685600	Weak transcription	Brain Substantia Nigra	brain
17	chr9:98673000-98685400	Weak transcription	NHDF-Ad	bronchial
18	chr9:98673600-98702200	Weak transcription	Small Intestine	intestine
19	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
20	chr9:98676600-98693200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:98677000-98685600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:98677200-98686200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:98677200-98688400	Strong transcription	A549	lung
24	chr9:98677400-98688400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr9:98677400-98688400	Strong transcription	Fetal Muscle Leg	muscle
26	chr9:98677400-98688800	Strong transcription	Dnd41	blood
27	chr9:98677600-98689000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:98677800-98686600	Strong transcription	Fetal Thymus	thymus
30	chr9:98677800-98687600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:98677800-98688800	Strong transcription	Adipose Nuclei	Adipose
32	chr9:98678000-98686200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:98678000-98688400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr9:98678000-98699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:98678000-98699600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:98678200-98686200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:98678200-98689200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:98678400-98688400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:98678400-98688800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:98678600-98705600	Weak transcription	Psoas Muscle	Psoas
41	chr9:98678800-98685600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:98679400-98685600	Weak transcription	Brain Germinal Matrix	brain
44	chr9:98679400-98685600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:98679400-98685600	Weak transcription	Lung	lung
46	chr9:98679400-98687400	Weak transcription	Colon Smooth Muscle	Colon
47	chr9:98679400-98695200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:98679400-98698600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:98680600-98686200	Strong transcription	Osteobl	bone
50	chr9:98680800-98685600	Weak transcription	K562	blood

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