Variant report

Variant	rs2421294
Chromosome Location	chr7:66816668-66816669
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11531446	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11533886	0.99[ASN][1000 genomes]
rs11543606	0.99[ASN][1000 genomes]
rs11543607	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11765091	0.99[ASN][1000 genomes]
rs11768377	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11768598	0.80[EUR][1000 genomes]
rs11773173	0.87[EUR][1000 genomes]
rs11983740	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12698577	0.99[ASN][1000 genomes]
rs13230948	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13238678	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13241524	0.86[EUR][1000 genomes]
rs13241865	0.87[EUR][1000 genomes]
rs17137359	0.86[EUR][1000 genomes]
rs17144911	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968149	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33999667	0.92[ASN][1000 genomes]
rs34167872	0.99[ASN][1000 genomes]
rs34671876	0.87[EUR][1000 genomes]
rs34858919	0.96[ASN][1000 genomes]
rs35858076	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140689	0.95[ASN][1000 genomes]
rs4140690	0.96[ASN][1000 genomes]
rs4717364	0.87[EUR][1000 genomes]
rs60285549	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466454	1.00[ASN][1000 genomes]
rs62466455	1.00[ASN][1000 genomes]
rs62467570	0.99[ASN][1000 genomes]
rs6956666	0.86[EUR][1000 genomes]
rs6960865	0.83[EUR][1000 genomes]
rs7341400	0.85[EUR][1000 genomes]
rs7804537	0.98[ASN][1000 genomes]
rs887715	0.83[EUR][1000 genomes]
rs9443	0.87[EUR][1000 genomes]
rs956523	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
4	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1031560	chr7:66805244-66846663	Enhancers Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1022779	chr7:66805244-66849392	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1031147	chr7:66811313-66922350	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2421294	STAG3L4	cis	Nerve Tibial	GTEx
rs2421294	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs2421294	STAG3L4	cis	Artery Aorta	GTEx
rs2421294	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs2421294	STAG3L4	cis	Esophagus Mucosa	GTEx
rs2421294	STAG3L4	cis	Thyroid	GTEx
rs2421294	STAG3L4	cis	lung	GTEx
rs2421294	STAG3L4	cis	Esophagus Muscularis	GTEx
rs2421294	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs2421294	STAG3L4	cis	Muscle Skeletal	GTEx
rs2421294	STAG3L4	cis	Whole Blood	GTEx
rs2421294	STAG3L4	cis	Artery Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66807200-66819600	Weak transcription	Brain Anterior Caudate	brain
2	chr7:66807200-66822400	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:66808400-66822200	Weak transcription	Right Ventricle	heart
4	chr7:66809800-66822600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:66809800-66822800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:66810000-66820800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr7:66810000-66822200	Weak transcription	Aorta	Aorta
8	chr7:66810000-66822200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:66810200-66816800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:66810200-66821400	Weak transcription	Ovary	ovary
11	chr7:66810200-66821600	Weak transcription	Adipose Nuclei	Adipose
12	chr7:66810200-66821800	Weak transcription	Liver	Liver
13	chr7:66810200-66822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:66810200-66822200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:66810200-66822800	Weak transcription	Brain Angular Gyrus	brain
16	chr7:66810200-66830400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:66810400-66819800	Weak transcription	Primary T cells from cord blood	blood
18	chr7:66810600-66821000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:66811200-66818000	Weak transcription	Left Ventricle	heart
20	chr7:66811200-66822000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:66811200-66822000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:66811600-66822800	Weak transcription	Brain Substantia Nigra	brain
23	chr7:66811600-66826000	Weak transcription	Psoas Muscle	Psoas
24	chr7:66813600-66821600	Weak transcription	Fetal Stomach	stomach
25	chr7:66815000-66817800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:66815200-66821000	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:66816200-66817800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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