Variant report

Variant	rs2721363
Chromosome Location	chr7:120626874-120626875
allele	A/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	SMC3	chr7:120626321-120630414	SK-N-SH	brain:	n/a	chr7:120628784-120628794 chr7:120627827-120627841
2	GATA1	chr7:120626486-120627991	PBDE	blood:	n/a	chr7:120627424-120627441 chr7:120627422-120627432
3	RAD21	chr7:120626694-120630432	SK-N-SH	brain:	n/a	chr7:120628734-120628747 chr7:120628739-120628752 chr7:120628735-120628749
4	RCOR1	chr7:120626647-120628237	K562	blood:	n/a	n/a
5	ARID3A	chr7:120626631-120626926	K562	blood:	n/a	n/a
6	RCOR1	chr7:120626702-120629554	K562	blood:	n/a	n/a
7	MXI1	chr7:120626776-120632296	SK-N-SH	brain:	n/a	n/a
8	EP300	chr7:120624468-120626977	SK-N-SH	brain:	n/a	chr7:120625228-120625235 chr7:120626631-120626641

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
2	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
CPED1	TF binding region
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10252911	0.85[CHB][hapmap]
rs10258025	0.81[EUR][1000 genomes]
rs10272601	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs10277935	0.86[ASW][hapmap];0.82[LWK][hapmap]
rs10464522	0.81[ASN][1000 genomes]
rs10953922	0.81[ASN][1000 genomes]
rs10953923	0.82[LWK][hapmap]
rs1557857	0.82[ASN][1000 genomes]
rs1859316	0.85[CHB][hapmap]
rs1859318	0.82[ASN][1000 genomes]
rs1859319	0.82[ASN][1000 genomes]
rs2074576	0.86[CEU][hapmap]
rs2074577	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap]
rs2244863	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244865	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248890	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2525705	0.82[ASN][1000 genomes]
rs2525709	0.81[ASN][1000 genomes]
rs2525712	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525713	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525717	0.84[CEU][hapmap]
rs2525718	0.86[CEU][hapmap]
rs2525719	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525722	0.85[CEU][hapmap]
rs2525729	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2525730	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525735	0.83[EUR][1000 genomes]
rs2525736	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525737	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525738	0.80[EUR][1000 genomes]
rs2525739	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs2525740	0.80[EUR][1000 genomes]
rs2525741	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525743	0.81[ASN][1000 genomes]
rs2721341	0.93[ASW][hapmap];0.81[ASN][1000 genomes]
rs2721351	0.85[CEU][hapmap]
rs2721354	0.93[ASW][hapmap];0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2721358	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721359	0.80[EUR][1000 genomes]
rs2721361	0.80[EUR][1000 genomes]
rs2721365	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721367	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721372	0.86[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757556	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs3779386	0.85[CHB][hapmap]
rs3823859	0.86[ASW][hapmap]
rs41688	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41689	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41690	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41703	0.81[EUR][1000 genomes]
rs41704	0.81[EUR][1000 genomes]
rs6466761	0.86[ASW][hapmap]
rs6466762	0.86[ASW][hapmap]
rs6949989	0.86[ASW][hapmap];0.82[LWK][hapmap]
rs6964344	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap]
rs6979247	0.85[CHB][hapmap]
rs745167	0.81[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap]
rs7781985	0.86[ASW][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2721363	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
2	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
3	chr7:120608600-120627600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:120609400-120627800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:120609400-120627800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:120609400-120628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:120611600-120627400	Weak transcription	Brain Angular Gyrus	brain
8	chr7:120611600-120627600	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:120611600-120627600	Weak transcription	Fetal Stomach	stomach
10	chr7:120611600-120627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:120611600-120627800	Weak transcription	Esophagus	oesophagus
12	chr7:120611600-120627800	Weak transcription	Thymus	Thymus
13	chr7:120615000-120627600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:120615400-120627800	Weak transcription	Colonic Mucosa	Colon
15	chr7:120615400-120628000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:120615600-120627400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:120615600-120627600	Weak transcription	Brain Anterior Caudate	brain
18	chr7:120615600-120627800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:120615600-120627800	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:120615600-120627800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:120615600-120628000	Weak transcription	Small Intestine	intestine
22	chr7:120615800-120627800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:120616000-120627400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:120616000-120627600	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:120616200-120627400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr7:120616200-120627400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:120616200-120627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:120616200-120627800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr7:120616200-120627800	Weak transcription	Fetal Intestine Large	intestine
30	chr7:120616600-120627600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:120616600-120627600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:120616800-120628000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:120617000-120627000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:120617000-120627800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr7:120617000-120627800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:120617200-120627800	Weak transcription	Adipose Nuclei	Adipose
37	chr7:120617200-120627800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr7:120617200-120627800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:120617200-120627800	Weak transcription	Left Ventricle	heart
40	chr7:120617400-120627800	Weak transcription	Liver	Liver
41	chr7:120617400-120627800	Weak transcription	Placenta	Placenta
42	chr7:120617400-120627800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr7:120617400-120627800	Weak transcription	HUVEC	blood vessel
44	chr7:120618000-120627800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr7:120620400-120627800	Weak transcription	Right Atrium	heart
46	chr7:120620800-120628600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr7:120622000-120627600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:120622000-120627800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:120622400-120627600	Weak transcription	HMEC	breast
50	chr7:120622400-120627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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