Variant report

Variant	rs56325879
Chromosome Location	chr7:66815581-66815582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAG3L4-6	chr7:66814559-66815590	NONHSAT121285

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10950072	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11761625	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11761686	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11765724	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34488927	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55672605	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs56266468	0.96[EUR][1000 genomes]
rs57236524	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73137799	0.85[EUR][1000 genomes]
rs73148491	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73148499	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73150480	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73152209	0.96[EUR][1000 genomes]
rs73152211	0.96[EUR][1000 genomes]
rs9647745	0.96[EUR][1000 genomes]
rs9647887	0.96[EUR][1000 genomes]
rs9647888	0.83[AFR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56325879	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66785800-66816200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr7:66805200-66816200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr7:66807200-66819600	Weak transcription	Brain Anterior Caudate	brain
4	chr7:66807200-66822400	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:66808400-66816200	Weak transcription	Thymus	Thymus
6	chr7:66808400-66822200	Weak transcription	Right Ventricle	heart
7	chr7:66808800-66815600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:66809800-66816000	Weak transcription	Dnd41	blood
9	chr7:66809800-66822600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:66809800-66822800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:66810000-66816400	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:66810000-66820800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr7:66810000-66822200	Weak transcription	Aorta	Aorta
14	chr7:66810000-66822200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:66810200-66816800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:66810200-66821400	Weak transcription	Ovary	ovary
17	chr7:66810200-66821600	Weak transcription	Adipose Nuclei	Adipose
18	chr7:66810200-66821800	Weak transcription	Liver	Liver
19	chr7:66810200-66822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:66810200-66822200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:66810200-66822800	Weak transcription	Brain Angular Gyrus	brain
22	chr7:66810200-66830400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:66810400-66815800	Weak transcription	Placenta	Placenta
24	chr7:66810400-66819800	Weak transcription	Primary T cells from cord blood	blood
25	chr7:66810600-66821000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:66811200-66818000	Weak transcription	Left Ventricle	heart
27	chr7:66811200-66822000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:66811200-66822000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:66811600-66822800	Weak transcription	Brain Substantia Nigra	brain
30	chr7:66811600-66826000	Weak transcription	Psoas Muscle	Psoas
31	chr7:66813400-66816200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:66813600-66821600	Weak transcription	Fetal Stomach	stomach
33	chr7:66815000-66817800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:66815200-66821000	Weak transcription	Fetal Muscle Leg	muscle

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