Variant report

Variant	rs6460209
Chromosome Location	chr7:64365918-64365919
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:64364987..64367738-chr7:64372489..64374310,3	K562	blood:
2	chr7:64365308..64368250-chr7:64464896..64466671,2	K562	blood:
3	chr7:64365012..64367238-chr7:64400877..64402549,2	MCF-7	breast:
4	chr7:64351381..64353400-chr7:64363667..64366418,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 42 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11773228	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11773456	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12532791	0.84[AMR][1000 genomes]
rs13223142	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13225933	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13236444	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13236784	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1830007	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1966140	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017252	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34238742	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35058955	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35065007	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3813700	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829003	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4644117	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4717222	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718154	0.85[AMR][1000 genomes]
rs4718156	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718169	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4718170	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56063644	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62455121	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62458435	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6953002	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6957266	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6965861	0.84[AMR][1000 genomes]
rs7776640	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7777724	0.83[AMR][1000 genomes]
rs7782713	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7786519	0.82[AMR][1000 genomes]
rs7796024	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7796284	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7797115	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7798063	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7798465	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7805817	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7811163	0.83[AMR][1000 genomes]
rs867630	0.82[AMR][1000 genomes]
rs9638209	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv1018967	chr7:64318129-64380869	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1019180	chr7:64329889-64512842	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv888283	chr7:64343985-64511564	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv2752165	chr7:64345822-65208605	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv970504	chr7:64361813-64366077	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs6460209	RP11-667F9.1	cis	Adipose Subcutaneous	GTEx
rs6460209	RP11-797H7.5	cis	lung	GTEx
rs6460209	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs6460209	CCT6P3	cis	Nerve Tibial	GTEx
rs6460209	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs6460209	RP11-797H7.5	cis	Stomach	GTEx
rs6460209	RP11-797H7.3	cis	Thyroid	GTEx
rs6460209	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs6460209	RP11-797H7.5	cis	Thyroid	GTEx
rs6460209	ERV3	cis	multi-tissue	Pritchard
rs6460209	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs6460209	CCT6P3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460209	RP11-797H7.3	cis	Whole Blood	GTEx
rs6460209	RP11-667F9.1	cis	Nerve Tibial	GTEx
rs6460209	RP11-797H7.3	cis	Stomach	GTEx
rs6460209	RP11-797H7.3	cis	Artery Tibial	GTEx
rs6460209	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs6460209	ZNF273	cis	lung	GTEx
rs6460209	ZNF273	cis	Heart Left Ventricle	GTEx
rs6460209	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs6460209	RP11-797H7.5	cis	Skin Sun Exposed Lower leg	GTEx
rs6460209	RP11-460N20.5	cis	Thyroid	GTEx
rs6460209	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs6460209	RP11-797H7.3	cis	lung	GTEx
rs6460209	RP11-797H7.5	cis	Adipose Subcutaneous	GTEx
rs6460209	RP11-797H7.5	cis	Artery Tibial	GTEx
rs6460209	RP11-460N20.5	cis	Nerve Tibial	GTEx
rs6460209	RP11-797H7.3	cis	Artery Aorta	GTEx
rs6460209	SEPHS1P1	cis	Nerve Tibial	GTEx
rs6460209	SEPHS1P1	cis	Thyroid	GTEx
rs6460209	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs6460209	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs6460209	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs6460209	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460209	RP11-797H7.5	cis	Heart Left Ventricle	GTEx
rs6460209	ZNF273	cis	Thyroid	GTEx
rs6460209	RP11-797H7.5	cis	Esophagus Muscularis	GTEx
rs6460209	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs6460209	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs6460209	RP11-460N20.5	cis	Whole Blood	GTEx
rs6460209	CCT6P3	cis	Esophagus Mucosa	GTEx
rs6460209	SEPHS1P1	cis	Artery Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64362800-64366000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:64362800-64366000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr7:64362800-64366400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:64363000-64366000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr7:64364200-64368200	Weak transcription	Left Ventricle	heart
6	chr7:64364200-64368800	Weak transcription	Pancreas	Pancrea
7	chr7:64364200-64380400	Weak transcription	Esophagus	oesophagus
8	chr7:64364400-64366200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr7:64364400-64366200	Enhancers	Fetal Brain Male	brain
10	chr7:64364400-64366800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:64364400-64367000	Weak transcription	HSMMtube	muscle
12	chr7:64364400-64367600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr7:64364400-64367800	Weak transcription	Psoas Muscle	Psoas
14	chr7:64364400-64368000	Weak transcription	Right Atrium	heart
15	chr7:64364400-64369600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:64364400-64376800	Weak transcription	Ovary	ovary
17	chr7:64364400-64379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:64364400-64380400	Weak transcription	Aorta	Aorta
19	chr7:64364400-64380400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:64364400-64382600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:64364600-64366000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:64364600-64366000	Flanking Active TSS	Dnd41	blood
23	chr7:64364600-64366200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:64364600-64366200	Enhancers	Primary T cells from cord blood	blood
25	chr7:64364600-64366200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:64364600-64366200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:64364600-64366200	Enhancers	HepG2	liver
28	chr7:64364600-64367000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:64364600-64367800	Weak transcription	NH-A	brain
30	chr7:64364600-64368000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:64364600-64368200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:64364600-64368200	Weak transcription	Stomach Mucosa	stomach
33	chr7:64364600-64368400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr7:64364600-64368400	Weak transcription	NHEK	skin
35	chr7:64364600-64372400	Weak transcription	Fetal Stomach	stomach
36	chr7:64364600-64374000	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:64364600-64383200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:64364600-64386400	Weak transcription	HUVEC	blood vessel
39	chr7:64364600-64387200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:64364800-64366000	Weak transcription	Lung	lung
41	chr7:64364800-64366000	Weak transcription	Hela-S3	cervix
42	chr7:64364800-64366400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:64364800-64367000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:64364800-64367000	Weak transcription	HSMM	muscle
45	chr7:64364800-64368200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:64364800-64368400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:64364800-64372400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:64364800-64373800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:64364800-64379200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:64364800-64379200	Weak transcription	Adipose Nuclei	Adipose

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