Variant report

Variant	rs73148491
Chromosome Location	chr7:66809672-66809673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66806712..66809740-chr7:66809964..66812550,3	K562	blood:
2	chr7:66808425..66811415-chr7:66821937..66824541,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAG3L4-1	chr7:66809042-66809767	NONHSAT121283

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10950072	0.90[EUR][1000 genomes]
rs11761625	0.86[EUR][1000 genomes]
rs11761686	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11765541	0.82[EUR][1000 genomes]
rs11765724	0.88[EUR][1000 genomes]
rs11766382	0.82[EUR][1000 genomes]
rs11768611	0.82[EUR][1000 genomes]
rs11770111	0.87[EUR][1000 genomes]
rs34488927	0.94[EUR][1000 genomes]
rs55672605	0.88[EUR][1000 genomes]
rs56266468	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56325879	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57236524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73148499	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73150480	0.91[EUR][1000 genomes]
rs73152209	0.88[EUR][1000 genomes]
rs73152211	0.88[EUR][1000 genomes]
rs9647745	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9647887	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9647888	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv966839	chr7:66805198-66815088	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv970413	chr7:66808251-66815088	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73148491	STAG3L4	cis	Heart Left Ventricle	GTEx
rs73148491	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66781400-66810200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:66785800-66816200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr7:66801200-66812000	Weak transcription	Gastric	stomach
4	chr7:66802600-66811800	Weak transcription	Stomach Mucosa	stomach
5	chr7:66802800-66814800	Weak transcription	HSMMtube	muscle
6	chr7:66803200-66811600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:66804400-66809800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:66804400-66810000	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr7:66804400-66810200	Strong transcription	Fetal Intestine Large	intestine
10	chr7:66804600-66809800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
11	chr7:66804600-66810400	Strong transcription	Primary T cells from cord blood	blood
12	chr7:66804600-66811200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr7:66805200-66816200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:66806200-66813400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:66806600-66810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:66807200-66811000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:66807200-66819600	Weak transcription	Brain Anterior Caudate	brain
18	chr7:66807200-66822400	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:66808000-66810200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr7:66808200-66810200	Strong transcription	Primary B cells from cord blood	blood
21	chr7:66808200-66810600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:66808400-66810000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
23	chr7:66808400-66810200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:66808400-66816200	Weak transcription	Thymus	Thymus
25	chr7:66808400-66822200	Weak transcription	Right Ventricle	heart
26	chr7:66808600-66809800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:66808600-66810000	ZNF genes & repeats	Aorta	Aorta
28	chr7:66808600-66810200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr7:66808800-66810000	Genic enhancers	Psoas Muscle	Psoas
30	chr7:66808800-66815600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr7:66809000-66810000	Strong transcription	Colon Smooth Muscle	Colon
32	chr7:66809000-66810400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:66809000-66810400	ZNF genes & repeats	NHEK	skin
34	chr7:66809000-66810600	ZNF genes & repeats	Fetal Stomach	stomach
35	chr7:66809000-66812400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr7:66809200-66809800	ZNF genes & repeats	Esophagus	oesophagus
37	chr7:66809200-66810000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:66809200-66810200	ZNF genes & repeats	Liver	Liver
39	chr7:66809200-66810200	ZNF genes & repeats	Ovary	ovary
40	chr7:66809200-66812400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:66809200-66813000	Weak transcription	Brain Germinal Matrix	brain
42	chr7:66809400-66809800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr7:66809400-66809800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:66809400-66809800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:66809400-66809800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:66809400-66809800	ZNF genes & repeats	Dnd41	blood
47	chr7:66809400-66810000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
48	chr7:66809400-66810000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:66809400-66810000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
50	chr7:66809400-66810000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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