Variant report

Variant	rs72864022
Chromosome Location	chr3:42645472-42645473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr3:42645181-42646156	U2OS	brain:	n/a	n/a
2	EGR1	chr3:42645399-42645681	K562	blood:	n/a	n/a
3	ZNF384	chr3:42644041-42645540	K562	blood:	n/a	n/a

Variant related genes	Relation type
SEC22C	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13064597	1.00[ASN][1000 genomes]
rs13067987	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085143	1.00[ASN][1000 genomes]
rs13100261	1.00[ASN][1000 genomes]
rs17030458	0.89[EUR][1000 genomes]
rs339705	0.80[EUR][1000 genomes]
rs34077739	1.00[ASN][1000 genomes]
rs34196076	1.00[ASN][1000 genomes]
rs34243788	1.00[ASN][1000 genomes]
rs35216140	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	1.00[ASN][1000 genomes]
rs35871059	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3900780	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[ASN][1000 genomes]
rs55994846	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58645732	1.00[ASN][1000 genomes]
rs58825152	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60535002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66933062	1.00[ASN][1000 genomes]
rs67174294	1.00[ASN][1000 genomes]
rs67583158	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67832425	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6797491	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71323162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616701	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623867	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72864022	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42642800-42646200	Weak transcription	Spleen	Spleen
2	chr3:42643000-42646200	Weak transcription	Pancreas	Pancrea
3	chr3:42643000-42650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:42643000-42650000	Weak transcription	Esophagus	oesophagus
5	chr3:42643200-42648400	Weak transcription	Placenta	Placenta
6	chr3:42643200-42649600	Weak transcription	Lung	lung
7	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:42643400-42647800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr3:42643600-42645600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:42643600-42648400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
12	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:42644000-42645600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:42644000-42645600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:42644000-42645600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:42644000-42645800	Enhancers	Liver	Liver
17	chr3:42644000-42645800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:42644000-42645800	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:42644000-42645800	Enhancers	A549	lung
20	chr3:42644000-42646200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:42644000-42646400	Weak transcription	Stomach Mucosa	stomach
22	chr3:42644000-42646800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:42644000-42647000	Weak transcription	Right Ventricle	heart
24	chr3:42644000-42647000	Enhancers	NHEK	skin
25	chr3:42644000-42647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:42644000-42647200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:42644000-42647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:42644000-42647600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:42644000-42648200	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:42644000-42648400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:42644000-42649800	Weak transcription	Right Atrium	heart
32	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
36	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:42644200-42645600	Genic enhancers	Fetal Intestine Small	intestine
38	chr3:42644200-42645600	Weak transcription	NHDF-Ad	bronchial
39	chr3:42644200-42645800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:42644200-42645800	ZNF genes & repeats	Dnd41	blood
41	chr3:42644200-42646000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:42644200-42646200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:42644200-42646200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:42644200-42646800	Weak transcription	HUVEC	blood vessel
45	chr3:42644200-42647000	Weak transcription	NHLF	lung
46	chr3:42644200-42647000	Weak transcription	Osteobl	bone
47	chr3:42644200-42648000	Weak transcription	Fetal Intestine Large	intestine
48	chr3:42644200-42648400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:42644200-42648400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:42644200-42648400	Weak transcription	Thymus	Thymus

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