Variant report

Variant	rs56067931
Chromosome Location	chr7:120481569-120481570
allele	C/T
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	POLR2A	chr7:120481216-120482040	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120477180..120479176-chr7:120481031..120482823,2	K562	blood:
2	chr7:120474789..120476459-chr7:120479485..120482303,2	K562	blood:

Variant related genes	Relation type
TSPAN12	TF binding region
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs114420	0.93[ASN][1000 genomes]
rs11976580	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12673417	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132731	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17142976	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17143013	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2189974	0.93[ASN][1000 genomes]
rs2525706	0.81[ASN][1000 genomes]
rs2525710	0.81[ASN][1000 genomes]
rs2721329	0.81[ASN][1000 genomes]
rs2721330	0.81[ASN][1000 genomes]
rs2721332	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721344	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721346	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721348	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721360	0.93[ASN][1000 genomes]
rs2721371	0.93[ASN][1000 genomes]
rs41613	1.00[ASN][1000 genomes]
rs41616	1.00[ASN][1000 genomes]
rs41617	1.00[ASN][1000 genomes]
rs41622	1.00[ASN][1000 genomes]
rs41623	1.00[ASN][1000 genomes]
rs41626	1.00[ASN][1000 genomes]
rs42333	1.00[ASN][1000 genomes]
rs4730982	1.00[ASN][1000 genomes]
rs55733320	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55749650	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56023697	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61481874	0.93[ASN][1000 genomes]
rs67679138	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73427871	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73427873	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73427878	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73721472	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7805733	1.00[ASN][1000 genomes]
rs7810542	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886440	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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
rs56067931	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:120466800-120482400	Weak transcription	Small Intestine	intestine
4	chr7:120468600-120482200	Weak transcription	Pancreas	Pancrea
5	chr7:120468600-120482400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:120468600-120483200	Weak transcription	Right Ventricle	heart
7	chr7:120468600-120487600	Weak transcription	Lung	lung
8	chr7:120470600-120484600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:120473800-120482000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:120474000-120482000	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:120474000-120482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:120474000-120482200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:120474000-120492400	Weak transcription	Fetal Lung	lung
14	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:120474600-120496600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:120476400-120484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:120476600-120482200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:120476600-120492400	Weak transcription	Gastric	stomach
19	chr7:120477000-120482200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:120477000-120482400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr7:120477000-120489800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:120477000-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:120477200-120496200	Weak transcription	Aorta	Aorta
24	chr7:120478000-120481800	Weak transcription	Fetal Intestine Small	intestine
25	chr7:120478000-120482200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:120478000-120483400	Weak transcription	Fetal Stomach	stomach
27	chr7:120478000-120483400	Weak transcription	Left Ventricle	heart
28	chr7:120478200-120482200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:120478200-120482200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:120478400-120487400	Weak transcription	Colonic Mucosa	Colon
31	chr7:120478800-120482400	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:120478800-120483200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:120479000-120482000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:120479200-120482000	Weak transcription	Fetal Kidney	kidney
35	chr7:120479200-120482200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:120479400-120484000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr7:120479400-120488000	Weak transcription	Right Atrium	heart
38	chr7:120479600-120481800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:120479600-120494000	Weak transcription	HUVEC	blood vessel
40	chr7:120479800-120481800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:120480000-120482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:120480000-120482600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:120480000-120488000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:120480200-120485000	Weak transcription	Fetal Heart	heart
45	chr7:120481000-120482800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr7:120481200-120482400	Genic enhancers	Fetal Intestine Large	intestine
47	chr7:120481200-120482600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr7:120481200-120482800	Enhancers	Liver	Liver
49	chr7:120481200-120482800	Enhancers	Stomach Mucosa	stomach
50	chr7:120481400-120481800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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