Variant report

Variant	rs6466759
Chromosome Location	chr7:120469690-120469691
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120467470..120469909-chr7:120470900..120473460,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10225453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252911	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10266755	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10272601	0.82[JPT][hapmap]
rs10274689	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10279837	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953922	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11982493	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669167	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231854	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17142976	0.85[CEU][hapmap]
rs17142995	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17143001	0.85[CEU][hapmap]
rs17143009	0.85[CEU][hapmap]
rs1859316	0.87[JPT][hapmap]
rs1859319	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2040762	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097806	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs2107275	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2107276	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2248890	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs2524949	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2524951	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2525709	0.80[ASN][1000 genomes]
rs2525743	0.80[ASN][1000 genomes]
rs2721339	0.83[EUR][1000 genomes]
rs2721341	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2721343	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721347	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721354	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs2721364	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3735467	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757556	0.82[JPT][hapmap]
rs3779386	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3814460	0.84[ASN][1000 genomes]
rs3823859	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823861	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41611	0.86[ASN][1000 genomes]
rs41621	0.91[ASN][1000 genomes]
rs41622	0.81[CEU][hapmap]
rs41624	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs41627	0.91[ASN][1000 genomes]
rs41628	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs41629	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs41631	0.81[ASN][1000 genomes]
rs41632	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4445165	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55855220	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61452531	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6466760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6466761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6466762	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953454	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958947	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6959328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964344	0.81[JPT][hapmap]
rs6964667	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6964786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971854	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6979247	0.91[JPT][hapmap]
rs714259	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs727228	0.82[CHB][hapmap]
rs73427805	0.84[ASN][1000 genomes]
rs73427866	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs745167	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7776721	0.91[JPT][hapmap]
rs7781985	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7800318	0.82[ASN][1000 genomes]
rs7805211	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7805733	0.81[CEU][hapmap]
rs7810542	0.95[CEU][hapmap]
rs996903	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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
rs6466759	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:120446000-120476200	Weak transcription	Left Ventricle	heart
5	chr7:120447400-120471400	Weak transcription	Fetal Kidney	kidney
6	chr7:120449800-120476000	Weak transcription	HUVEC	blood vessel
7	chr7:120450600-120470400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:120452800-120476000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:120455600-120472200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr7:120455800-120474400	Weak transcription	Fetal Intestine Large	intestine
11	chr7:120455800-120476000	Weak transcription	Fetal Muscle Leg	muscle
12	chr7:120458400-120475800	Weak transcription	Fetal Intestine Small	intestine
13	chr7:120464000-120476000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:120466000-120473600	Weak transcription	Fetal Lung	lung
15	chr7:120466000-120479600	Weak transcription	Ovary	ovary
16	chr7:120466400-120470600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:120466600-120476200	Weak transcription	Gastric	stomach
18	chr7:120466800-120482400	Weak transcription	Small Intestine	intestine
19	chr7:120467000-120476200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:120468200-120470200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr7:120468200-120472400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:120468200-120473800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:120468400-120472200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:120468400-120472400	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:120468400-120479000	Weak transcription	Fetal Heart	heart
26	chr7:120468600-120471400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:120468600-120472200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:120468600-120475800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:120468600-120477000	Weak transcription	Fetal Stomach	stomach
30	chr7:120468600-120482200	Weak transcription	Pancreas	Pancrea
31	chr7:120468600-120482400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:120468600-120483200	Weak transcription	Right Ventricle	heart
33	chr7:120468600-120487600	Weak transcription	Lung	lung
34	chr7:120468800-120472400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:120468800-120476000	Weak transcription	Aorta	Aorta
36	chr7:120469000-120469800	Active TSS	Liver	Liver
37	chr7:120469000-120470000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr7:120469200-120469800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr7:120469200-120469800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr7:120469400-120469800	Active TSS	Duodenum Mucosa	Duodenum
41	chr7:120469400-120469800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr7:120469400-120470200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr7:120469600-120469800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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