Variant report

Variant	rs2248890
Chromosome Location	chr7:120597993-120597994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120596918..120600663-chr7:120601555..120604578,6	MCF-7	breast:
2	chr7:120589571..120591226-chr7:120597361..120599161,2	MCF-7	breast:
3	chr7:120439909..120442311-chr7:120595170..120598046,2	K562	blood:
4	chr7:120597607..120599644-chr7:120678878..120681587,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10225453	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs10252911	0.90[CHB][hapmap]
rs10272601	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10274689	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10953922	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12706306	0.82[YRI][hapmap]
rs1557857	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17142995	0.80[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs17143001	0.85[CEU][hapmap]
rs17143009	0.85[CEU][hapmap]
rs1859316	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1859318	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1859319	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2040762	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2074577	0.95[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2097806	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs2107276	0.80[CHB][hapmap]
rs2244863	0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2244865	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2524951	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2525705	0.90[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2525709	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2525710	0.85[CEU][hapmap]
rs2525712	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525713	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525719	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525729	0.81[AMR][1000 genomes]
rs2525730	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2525736	0.84[ASN][1000 genomes]
rs2525737	0.89[ASN][1000 genomes]
rs2525741	0.84[ASN][1000 genomes]
rs2525743	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2721330	0.86[CEU][hapmap]
rs2721332	0.81[CEU][hapmap]
rs2721339	0.82[AMR][1000 genomes]
rs2721341	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2721347	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2721354	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]
rs2721358	0.81[ASN][1000 genomes]
rs2721363	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2721365	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2721367	0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2721372	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3757556	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3779386	0.90[CHB][hapmap]
rs3823859	0.80[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3823861	0.81[JPT][hapmap]
rs41624	0.81[JPT][hapmap]
rs41629	0.81[JPT][hapmap]
rs41632	0.81[JPT][hapmap]
rs41688	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs41689	0.84[ASN][1000 genomes]
rs41690	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs6466759	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs6466760	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs6466761	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs6466762	0.80[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6953454	0.86[JPT][hapmap]
rs6959328	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs6964344	0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap]
rs6979247	0.80[CHB][hapmap]
rs714259	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs745167	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7776721	0.80[CHB][hapmap]
rs7781985	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs996903	0.85[JPT][hapmap]

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	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
rs2248890	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120600200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:120591600-120606600	Weak transcription	Lung	lung
3	chr7:120591600-120608000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:120591600-120608000	Weak transcription	Esophagus	oesophagus
5	chr7:120591600-120608000	Weak transcription	Gastric	stomach
6	chr7:120591600-120608000	Weak transcription	Spleen	Spleen
7	chr7:120591600-120611200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:120591600-120612800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:120591600-120613200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:120591600-120613200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
12	chr7:120591800-120606400	Weak transcription	Ovary	ovary
13	chr7:120591800-120618600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:120592200-120598400	Weak transcription	Thymus	Thymus
15	chr7:120592200-120599400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:120592200-120599600	Strong transcription	Fetal Thymus	thymus
17	chr7:120592200-120611000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:120592400-120598600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:120592400-120598600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:120592400-120599400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:120592400-120600200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr7:120592400-120606400	Weak transcription	Fetal Brain Male	brain
23	chr7:120592400-120606400	Weak transcription	NHEK	skin
24	chr7:120592400-120607800	Weak transcription	HSMMtube	muscle
25	chr7:120592400-120608000	Weak transcription	Psoas Muscle	Psoas
26	chr7:120592400-120614800	Weak transcription	Small Intestine	intestine
27	chr7:120592400-120617000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr7:120592400-120618600	Weak transcription	Right Ventricle	heart
29	chr7:120592400-120621600	Weak transcription	Aorta	Aorta
30	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
31	chr7:120592800-120598000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:120593000-120599600	Strong transcription	Placenta	Placenta
33	chr7:120593000-120604600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr7:120593000-120606400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr7:120593200-120599000	Weak transcription	Fetal Heart	heart
36	chr7:120593200-120599400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:120593200-120599400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr7:120593200-120599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:120593200-120599800	Strong transcription	HSMM	muscle
40	chr7:120593200-120599800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:120593400-120598000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:120593400-120598200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:120593400-120598400	Strong transcription	K562	blood
44	chr7:120593400-120599400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:120593400-120599400	Strong transcription	Liver	Liver
46	chr7:120593400-120599600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:120593400-120599600	Strong transcription	Fetal Intestine Large	intestine
48	chr7:120593400-120600400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr7:120593600-120602000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr7:120593800-120598000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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