Variant report

Variant	rs2721354
Chromosome Location	chr7:120592007-120592008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120494775..120497431-chr7:120590834..120592743,2	K562	blood:
2	chr7:120495769..120499665-chr7:120588624..120592417,7	MCF-7	breast:
3	chr7:120588429..120592994-chr7:120712560..120717211,6	K562	blood:
4	chr7:120589475..120592677-chr7:120719093..120725846,11	K562	blood:
5	chr7:120588468..120596180-chr7:120604298..120610010,9	MCF-7	breast:
6	chr7:120589600..120593889-chr7:120719099..120726294,8	K562	blood:
7	chr7:120591610..120593367-chr7:120598953..120601723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000071243	Chromatin interaction
ENSG00000106025	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10225453	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs10238554	0.83[ASN][1000 genomes]
rs10252911	0.90[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10266755	0.82[JPT][hapmap]
rs10272601	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10274689	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10277935	0.80[ASW][hapmap]
rs10279837	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10282072	0.83[ASN][1000 genomes]
rs10953922	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11982493	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12706306	0.81[YRI][hapmap]
rs1557857	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17142995	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs17143001	0.85[CEU][hapmap]
rs17143009	0.85[CEU][hapmap]
rs1859316	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1859318	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1859319	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2040762	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058501	0.81[LWK][hapmap]
rs2074577	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2097806	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2107276	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs2244863	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2244865	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2248890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2524949	0.81[EUR][1000 genomes]
rs2524951	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2525705	0.90[CEU][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2525708	0.81[ASN][1000 genomes]
rs2525709	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525710	0.85[CEU][hapmap]
rs2525712	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525713	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525719	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525730	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2525736	0.81[ASN][1000 genomes]
rs2525737	0.89[ASN][1000 genomes]
rs2525741	0.81[ASN][1000 genomes]
rs2525743	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721330	0.85[CEU][hapmap]
rs2721332	0.81[CEU][hapmap]
rs2721339	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2721341	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721343	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2721347	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2721363	0.93[ASW][hapmap];0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2721364	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2721365	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2721367	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2721372	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3757556	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3779386	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs3823859	0.93[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs3823861	0.86[JPT][hapmap]
rs41624	0.86[JPT][hapmap]
rs41629	0.86[JPT][hapmap]
rs41632	0.86[JPT][hapmap]
rs41688	0.89[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs41689	0.81[ASN][1000 genomes]
rs41690	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs61452531	0.84[ASN][1000 genomes]
rs6466759	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs6466760	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs6466761	0.93[ASW][hapmap];0.80[CEU][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap]
rs6466762	0.93[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs6944789	0.81[LWK][hapmap]
rs6949989	0.80[ASW][hapmap]
rs6953454	0.90[JPT][hapmap]
rs6959328	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs6964344	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6971854	0.90[CHB][hapmap]
rs6979247	0.90[CHB][hapmap]
rs714259	0.95[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap];0.81[EUR][1000 genomes]
rs732568	0.81[ASN][1000 genomes]
rs73427866	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs745167	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776721	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs7781985	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap]
rs996903	0.87[ASW][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2721354	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120589400-120592400	Active TSS	A549	lung
2	chr7:120589600-120592200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:120589800-120592400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:120589800-120592400	Active TSS	NHLF	lung
5	chr7:120590000-120592200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:120590000-120592200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:120590000-120592400	Active TSS	Psoas Muscle	Psoas
8	chr7:120590000-120592400	Active TSS	Right Ventricle	heart
9	chr7:120591200-120592200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:120591200-120592200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
11	chr7:120591200-120592400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:120591400-120592200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:120591400-120592200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr7:120591400-120592200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr7:120591400-120592200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr7:120591400-120592200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr7:120591400-120592200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr7:120591400-120592200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:120591400-120592200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:120591400-120592200	Flanking Active TSS	Liver	Liver
21	chr7:120591400-120592200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr7:120591400-120592200	Flanking Active TSS	NHEK	skin
23	chr7:120591400-120592400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:120591400-120592400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr7:120591400-120592400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr7:120591400-120592400	Active TSS	Right Atrium	heart
27	chr7:120591400-120592400	Flanking Active TSS	HMEC	breast
28	chr7:120591400-120592400	Flanking Active TSS	HUVEC	blood vessel
29	chr7:120591400-120592400	Flanking Active TSS	NH-A	brain
30	chr7:120591600-120592200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:120591600-120592200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr7:120591600-120592200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr7:120591600-120592200	Flanking Active TSS	Fetal Heart	heart
34	chr7:120591600-120592200	Enhancers	Placenta	Placenta
35	chr7:120591600-120592200	Flanking Active TSS	HSMMtube	muscle
36	chr7:120591600-120592200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr7:120591600-120592200	Flanking Active TSS	Osteobl	bone
38	chr7:120591600-120592400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:120591600-120592400	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr7:120591600-120592400	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr7:120591600-120592400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr7:120591600-120592400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr7:120591600-120596400	Weak transcription	Left Ventricle	heart
44	chr7:120591600-120600200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:120591600-120606600	Weak transcription	Lung	lung
46	chr7:120591600-120608000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:120591600-120608000	Weak transcription	Esophagus	oesophagus
48	chr7:120591600-120608000	Weak transcription	Gastric	stomach
49	chr7:120591600-120608000	Weak transcription	Spleen	Spleen
50	chr7:120591600-120611200	Weak transcription	Placenta Amnion	Placenta Amnion

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