Variant report

Variant	rs35307336
Chromosome Location	chr7:66781776-66781777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11760794	0.92[ASN][1000 genomes]
rs11760843	0.94[ASN][1000 genomes]
rs11760899	0.92[ASN][1000 genomes]
rs11762397	0.92[ASN][1000 genomes]
rs11763894	0.94[ASN][1000 genomes]
rs11768598	0.87[ASN][1000 genomes]
rs11769438	0.83[ASN][1000 genomes]
rs11770307	0.84[ASN][1000 genomes]
rs11771920	0.92[ASN][1000 genomes]
rs11772041	0.95[ASN][1000 genomes]
rs11772331	0.95[ASN][1000 genomes]
rs11773173	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698575	0.95[ASN][1000 genomes]
rs13226941	0.95[ASN][1000 genomes]
rs13241524	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13241865	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17137359	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1968150	0.92[ASN][1000 genomes]
rs34037266	0.92[ASN][1000 genomes]
rs34671876	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35565843	0.89[ASN][1000 genomes]
rs35715970	0.92[ASN][1000 genomes]
rs36146582	0.87[ASN][1000 genomes]
rs4236211	0.86[ASN][1000 genomes]
rs4590320	0.84[ASN][1000 genomes]
rs4717364	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718534	0.95[ASN][1000 genomes]
rs4718536	0.95[ASN][1000 genomes]
rs4718559	0.83[ASN][1000 genomes]
rs55777645	0.95[ASN][1000 genomes]
rs62466443	0.95[ASN][1000 genomes]
rs62467577	0.89[ASN][1000 genomes]
rs6956666	0.89[ASN][1000 genomes]
rs6960865	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6963583	0.95[ASN][1000 genomes]
rs71565103	0.94[ASN][1000 genomes]
rs71565104	0.94[ASN][1000 genomes]
rs7341400	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7786846	0.87[ASN][1000 genomes]
rs7788177	0.95[ASN][1000 genomes]
rs7804093	0.87[ASN][1000 genomes]
rs887715	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9443	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs956523	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs35307336	STAG3L4	cis	Esophagus Muscularis	GTEx
rs35307336	STAG3L4	cis	Heart Left Ventricle	GTEx
rs35307336	STAG3L4	cis	Stomach	GTEx
rs35307336	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs35307336	STAG3L4	cis	Whole Blood	GTEx
rs35307336	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs35307336	STAG3L4	cis	Artery Tibial	GTEx
rs35307336	STAG3L4	cis	Thyroid	GTEx
rs35307336	STAG3L4	cis	Nerve Tibial	GTEx
rs35307336	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs35307336	STAG3L4	cis	Muscle Skeletal	GTEx
rs35307336	STAG3L4	cis	lung	GTEx
rs35307336	STAG3L4	cis	Artery Aorta	GTEx
rs35307336	STAG3L4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66768600-66782400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66768800-66783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66768800-66783400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:66769000-66785400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:66769400-66782800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:66769400-66783400	Strong transcription	Primary T cells from cord blood	blood
7	chr7:66769400-66785000	Strong transcription	Fetal Stomach	stomach
8	chr7:66769400-66785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:66770000-66782800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:66770000-66783000	Strong transcription	Duodenum Mucosa	Duodenum
11	chr7:66770000-66783400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr7:66770000-66785400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr7:66770200-66783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:66770200-66785800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:66770400-66783400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:66770400-66783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:66770400-66783600	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:66770400-66786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:66770600-66782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:66770600-66785200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr7:66770600-66785400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:66770600-66786400	Weak transcription	Fetal Heart	heart
24	chr7:66770800-66783400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr7:66770800-66786800	Strong transcription	Liver	Liver
26	chr7:66771000-66785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:66771200-66781800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr7:66771200-66785000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:66771200-66785000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:66771400-66783000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr7:66771400-66785600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:66771600-66783000	Strong transcription	Left Ventricle	heart
33	chr7:66771800-66783400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:66771800-66786000	Strong transcription	Fetal Intestine Large	intestine
35	chr7:66771800-66786200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr7:66772200-66783200	Strong transcription	Spleen	Spleen
37	chr7:66772200-66786200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr7:66772400-66781800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr7:66772400-66783000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr7:66772400-66783000	Strong transcription	Dnd41	blood
41	chr7:66772400-66783600	Strong transcription	Fetal Muscle Leg	muscle
42	chr7:66772600-66782200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:66772600-66785600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:66772600-66786200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr7:66773000-66782800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr7:66773200-66782000	Strong transcription	HSMMtube	muscle
47	chr7:66774200-66783000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:66774200-66785800	Weak transcription	Stomach Mucosa	stomach
49	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
50	chr7:66775400-66784400	Weak transcription	Psoas Muscle	Psoas

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