Variant report

Variant	rs62453511
Chromosome Location	chr7:7210121-7210122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10447684	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13238772	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17164011	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17249770	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17250084	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17309555	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2116533	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2116534	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2116535	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163638	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163639	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34386799	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34419200	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34491888	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34705126	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34971257	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4324853	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4428582	0.87[EUR][1000 genomes]
rs4582461	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58312319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58843310	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61465425	0.80[EUR][1000 genomes]
rs62449960	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62449964	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62449965	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453487	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62453491	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62453504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453505	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453506	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453507	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62453510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62453512	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62453513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9648103	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv428160	chr7:6936949-7219553	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1020929	chr7:6954959-7232920	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	nsv464300	chr7:7040176-7368699	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv606033	chr7:7040176-7368699	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv1016369	chr7:7053923-7375567	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv1023788	chr7:7053923-7407783	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv538720	chr7:7053923-7407783	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
14	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
16	nsv1032974	chr7:7145831-7393218	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
18	nsv508445	chr7:7190518-7261098	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
19	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
20	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62453511	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7198200-7212800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:7198800-7211800	Weak transcription	Osteobl	bone
3	chr7:7199600-7212400	Weak transcription	HSMM	muscle
4	chr7:7205000-7210200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:7205000-7211000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:7205400-7212600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:7205600-7211800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:7205600-7214600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:7205800-7220800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:7205800-7220800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:7207600-7211200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:7208000-7212600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:7208000-7216600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:7209400-7211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:7209400-7211800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr7:7210000-7210400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:7210000-7212400	Weak transcription	HepG2	liver

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