Variant report

Variant	rs6788543
Chromosome Location	chr3:111458837-111458838
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111457259..111459990-chr3:111577947..111581239,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10470303	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10804492	0.81[CHD][hapmap]
rs11710738	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11711533	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11711582	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12330761	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490166	0.98[GIH][hapmap]
rs12632310	0.82[JPT][hapmap]
rs13074817	0.98[GIH][hapmap]
rs13079085	0.98[GIH][hapmap]
rs2137595	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs4284954	0.98[GIH][hapmap]
rs4401340	0.96[TSI][hapmap]
rs4413291	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs4431081	0.98[GIH][hapmap]
rs4557129	0.81[CHD][hapmap]
rs4682057	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682298	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4682299	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682305	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4682312	0.84[CEU][hapmap]
rs4682314	0.84[CEU][hapmap]
rs56028731	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62273780	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62275532	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438003	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6768713	0.98[GIH][hapmap]
rs6784753	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6786612	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6796087	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7609653	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7629156	0.81[CHD][hapmap]
rs955381	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959540	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9818574	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9823974	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9834030	0.98[GIH][hapmap]
rs9868171	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868909	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9870656	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6788543	CCDC80	cis	parietal	SCAN
rs6788543	CD96	cis	lymphoblastoid	seeQTL
rs6788543	ZBED2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:111452800-111459200	Enhancers	Osteobl	bone
3	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
6	chr3:111454600-111459400	Enhancers	HepG2	liver
7	chr3:111454600-111459600	Enhancers	Liver	Liver
8	chr3:111454800-111460400	Enhancers	Fetal Heart	heart
9	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
10	chr3:111455000-111461000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:111455800-111459000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:111455800-111459200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:111455800-111461000	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:111456000-111459000	Enhancers	Fetal Muscle Leg	muscle
15	chr3:111456000-111459000	Enhancers	Stomach Mucosa	stomach
16	chr3:111456200-111459000	Flanking Active TSS	A549	lung
17	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
18	chr3:111456400-111459000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:111456400-111459000	Weak transcription	Gastric	stomach
20	chr3:111457000-111459000	Enhancers	NHLF	lung
21	chr3:111457000-111459200	Enhancers	NH-A	brain
22	chr3:111457400-111459200	Enhancers	HSMM	muscle
23	chr3:111457400-111460200	Weak transcription	Fetal Kidney	kidney
24	chr3:111457600-111459000	Enhancers	HUVEC	blood vessel
25	chr3:111457600-111459200	Enhancers	Left Ventricle	heart
26	chr3:111457600-111459200	Enhancers	Pancreas	Pancrea
27	chr3:111457600-111459200	Flanking Active TSS	NHEK	skin
28	chr3:111458000-111459400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:111458000-111467000	Weak transcription	Right Ventricle	heart
30	chr3:111458200-111459200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:111458400-111459200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:111458600-111459000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:111458600-111459800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:111458600-111459800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:111458600-111460000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:111458600-111460400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:111458600-111462200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:111458600-111464400	Weak transcription	Psoas Muscle	Psoas
39	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:111458800-111459000	Enhancers	Brain Hippocampus Middle	brain
41	chr3:111458800-111459000	Enhancers	Colon Smooth Muscle	Colon
42	chr3:111458800-111459000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr3:111458800-111459000	Flanking Active TSS	HMEC	breast
44	chr3:111458800-111459200	Enhancers	Esophagus	oesophagus
45	chr3:111458800-111459800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:111458800-111459800	Enhancers	Hela-S3	cervix
47	chr3:111458800-111461800	Weak transcription	Adipose Nuclei	Adipose
48	chr3:111458800-111464800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:111458800-111466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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