Variant report

Variant	rs6769931
Chromosome Location	chr3:53160193-53160194
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53159175..53161619-chr3:53212406..53215272,2	MCF-7	breast:
2	chr3:53159803..53162439-chr3:53162979..53165475,2	K562	blood:
3	chr3:53137358..53139996-chr3:53159100..53161040,2	K562	blood:
4	chr3:53159864..53162439-chr3:53163975..53165914,2	K562	blood:
5	chr3:53160152..53162531-chr3:53170013..53171718,2	K562	blood:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1004807	0.82[EUR][1000 genomes]
rs11130341	0.83[EUR][1000 genomes]
rs12630819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319872	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13433700	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560332	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2253675	0.83[ASN][1000 genomes]
rs2336724	0.83[ASN][1000 genomes]
rs2564922	0.83[ASN][1000 genomes]
rs2564929	0.96[ASN][1000 genomes]
rs2564944	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581798	0.84[ASN][1000 genomes]
rs28501212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28734933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796351	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4282053	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687570	0.85[EUR][1000 genomes]
rs55950520	0.96[ASN][1000 genomes]
rs56058643	0.96[ASN][1000 genomes]
rs56386026	0.96[ASN][1000 genomes]
rs57261253	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57514626	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61296683	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62255925	0.96[ASN][1000 genomes]
rs62255926	0.88[ASN][1000 genomes]
rs62255929	0.96[ASN][1000 genomes]
rs62255931	0.96[ASN][1000 genomes]
rs6445565	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445566	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6769944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777975	0.89[EUR][1000 genomes]
rs6783748	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784207	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792345	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792363	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6799837	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6809973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73082047	0.84[ASN][1000 genomes]
rs73088322	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73088327	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73088342	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615099	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs891369	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930122	0.83[ASN][1000 genomes]
rs9757079	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817467	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9820125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820324	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824325	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9828221	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9830353	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834111	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9838517	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9844531	0.85[EUR][1000 genomes]
rs9845021	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9845352	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9845484	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861744	0.82[EUR][1000 genomes]
rs9867023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867590	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9868263	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868406	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872260	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6769931	RFT1	cis	Artery Aorta	GTEx
rs6769931	RFT1	cis	Artery Tibial	GTEx
rs6769931	SERBP1P3	cis	Thyroid	GTEx
rs6769931	RFT1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53137400-53161600	Strong transcription	Fetal Intestine Small	intestine
2	chr3:53142800-53161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53145000-53161400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:53145800-53161200	Strong transcription	Primary hematopoietic stem cells	blood
5	chr3:53147600-53160800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:53148000-53163600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:53148200-53160600	Strong transcription	Fetal Intestine Large	intestine
8	chr3:53148200-53161000	Strong transcription	Fetal Thymus	thymus
9	chr3:53148400-53160200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:53148400-53160400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:53148400-53160800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:53148400-53161000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:53148400-53161000	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:53148400-53161200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:53148400-53161200	Strong transcription	Dnd41	blood
16	chr3:53148400-53161600	Strong transcription	Primary T cells from cord blood	blood
17	chr3:53148400-53163400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:53148600-53160200	Strong transcription	Brain Hippocampus Middle	brain
19	chr3:53148600-53160200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr3:53148600-53160400	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:53148600-53160800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:53148600-53161200	Strong transcription	Liver	Liver
23	chr3:53148800-53160200	Strong transcription	Fetal Lung	lung
24	chr3:53148800-53160400	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:53148800-53161200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:53149200-53160400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:53149200-53161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:53149400-53160200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:53149400-53160200	Strong transcription	Fetal Brain Female	brain
30	chr3:53149400-53160400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:53149400-53160400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:53149600-53161400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:53149600-53162400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:53150000-53161800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:53150800-53160400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:53150800-53160400	Strong transcription	HepG2	liver
37	chr3:53150800-53160800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:53150800-53161000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:53151000-53160200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:53151000-53160200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:53151000-53160200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:53151000-53160200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:53151000-53160400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:53151000-53160600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:53151000-53160800	Strong transcription	HMEC	breast
46	chr3:53151000-53160800	Strong transcription	NHLF	lung
47	chr3:53151000-53161000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:53151000-53161000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:53151000-53161000	Strong transcription	NHEK	skin
50	chr3:53151000-53161000	Strong transcription	Osteobl	bone

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