Variant report

Variant	rs55749650
Chromosome Location	chr7:120493938-120493939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120492091..120494339-chr7:120499581..120501405,2	K562	blood:
2	chr7:120490293..120494188-chr7:120496903..120500277,5	MCF-7	breast:
3	chr7:120493325..120495298-chr7:120504953..120507173,2	K562	blood:
4	chr7:120491569..120493974-chr7:120494829..120497807,2	MCF-7	breast:
5	chr7:120489201..120491293-chr7:120493630..120496553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs114420	0.82[ASN][1000 genomes]
rs11976580	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12673417	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17132731	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17142976	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17143013	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2189974	0.82[ASN][1000 genomes]
rs2721332	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2721344	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2721346	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2721348	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2721360	0.82[ASN][1000 genomes]
rs2721371	0.82[ASN][1000 genomes]
rs41613	0.88[ASN][1000 genomes]
rs41616	0.88[ASN][1000 genomes]
rs41617	0.88[ASN][1000 genomes]
rs41622	0.88[ASN][1000 genomes]
rs41623	0.88[ASN][1000 genomes]
rs41626	0.88[ASN][1000 genomes]
rs42333	0.88[ASN][1000 genomes]
rs4730982	0.88[ASN][1000 genomes]
rs55733320	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56023697	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56067931	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61481874	0.82[ASN][1000 genomes]
rs67679138	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73427871	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73427873	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73427878	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73721472	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7805733	0.88[ASN][1000 genomes]
rs7810542	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs886440	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55749650	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:120474600-120496600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:120477200-120496200	Weak transcription	Aorta	Aorta
5	chr7:120479600-120494000	Weak transcription	HUVEC	blood vessel
6	chr7:120482600-120495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:120482600-120496200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:120482800-120496400	Weak transcription	Liver	Liver
9	chr7:120482800-120496400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:120482800-120496600	Weak transcription	Stomach Mucosa	stomach
11	chr7:120483400-120496200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:120483400-120496400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:120483600-120496600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:120485200-120496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:120485200-120496200	Weak transcription	Fetal Stomach	stomach
16	chr7:120485200-120496600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:120485200-120496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:120485400-120496400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:120485400-120496400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:120487600-120495000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:120488200-120494800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:120488200-120496200	Weak transcription	Fetal Intestine Small	intestine
23	chr7:120488200-120496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:120488200-120496600	Weak transcription	Colonic Mucosa	Colon
25	chr7:120488400-120496000	Weak transcription	Fetal Kidney	kidney
26	chr7:120488400-120496200	Weak transcription	Right Ventricle	heart
27	chr7:120488600-120495200	Weak transcription	Fetal Intestine Large	intestine
28	chr7:120489200-120496200	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:120489400-120495600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:120490200-120495800	Weak transcription	Left Ventricle	heart
31	chr7:120490600-120494200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:120490600-120495800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:120490600-120496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:120490600-120496800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:120492000-120495200	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:120492600-120494200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:120492800-120496200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:120492800-120496400	Weak transcription	Fetal Lung	lung
39	chr7:120492800-120496600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:120492800-120496600	Weak transcription	Gastric	stomach
41	chr7:120493000-120494200	Weak transcription	Fetal Heart	heart
42	chr7:120493000-120496200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:120493000-120496200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr7:120493000-120496400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:120493400-120494400	Weak transcription	GM12878-XiMat	blood
46	chr7:120493800-120495200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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