Variant report

Variant	rs6466761
Chromosome Location	chr7:120474168-120474169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120457748..120459607-chr7:120472145..120474237,2	K562	blood:
2	chr7:120467426..120469359-chr7:120473701..120476319,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10225453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10252911	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10266755	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10272601	0.81[JPT][hapmap]
rs10274689	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[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];0.92[ASN][1000 genomes]
rs10953922	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10953923	0.80[ASW][hapmap]
rs11982493	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12669167	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13231854	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17142976	0.85[CEU][hapmap]
rs17142995	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17143001	0.85[CEU][hapmap]
rs17143009	0.85[CEU][hapmap]
rs1859316	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1859319	0.80[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]
rs2074577	0.86[ASW][hapmap]
rs2097806	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs2107275	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2189452	0.81[CHD][hapmap]
rs2244863	0.86[ASW][hapmap]
rs2248890	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs2524949	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2524951	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2525709	0.81[ASN][1000 genomes]
rs2525743	0.81[ASN][1000 genomes]
rs2721339	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2721341	0.93[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2721343	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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];0.92[ASN][1000 genomes]
rs2721354	0.93[ASW][hapmap];0.80[CEU][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap]
rs2721363	0.86[ASW][hapmap]
rs2721364	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3735467	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757556	0.81[JPT][hapmap]
rs3779386	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs3814460	0.85[ASN][1000 genomes]
rs3823859	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823861	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41611	0.85[ASN][1000 genomes]
rs41621	0.91[ASN][1000 genomes]
rs41622	0.81[CEU][hapmap]
rs41624	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs41627	0.91[ASN][1000 genomes]
rs41628	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs41629	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs41631	0.80[ASN][1000 genomes]
rs41632	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41690	0.86[ASW][hapmap]
rs4445165	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55855220	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61452531	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6466759	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]
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]
rs6466762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6944789	0.80[ASW][hapmap]
rs6953454	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6958947	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6964344	0.81[JPT][hapmap]
rs6964667	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6964786	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6979247	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs714259	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs727228	0.81[CHB][hapmap]
rs73427805	0.85[ASN][1000 genomes]
rs73427866	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs745167	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7781985	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800318	0.83[ASN][1000 genomes]
rs7805211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805733	0.81[CEU][hapmap]
rs7810542	0.95[CEU][hapmap]
rs996903	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6466761	TSPAN12	cis	Artery Tibial	GTEx
rs6466761	TSPAN12	cis	parietal	SCAN

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

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	chr7:120446000-120476200	Weak transcription	Left Ventricle	heart
4	chr7:120449800-120476000	Weak transcription	HUVEC	blood vessel
5	chr7:120452800-120476000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:120455800-120474400	Weak transcription	Fetal Intestine Large	intestine
7	chr7:120455800-120476000	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:120458400-120475800	Weak transcription	Fetal Intestine Small	intestine
9	chr7:120464000-120476000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:120466000-120479600	Weak transcription	Ovary	ovary
11	chr7:120466600-120476200	Weak transcription	Gastric	stomach
12	chr7:120466800-120482400	Weak transcription	Small Intestine	intestine
13	chr7:120467000-120476200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:120468400-120479000	Weak transcription	Fetal Heart	heart
15	chr7:120468600-120475800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:120468600-120477000	Weak transcription	Fetal Stomach	stomach
17	chr7:120468600-120482200	Weak transcription	Pancreas	Pancrea
18	chr7:120468600-120482400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:120468600-120483200	Weak transcription	Right Ventricle	heart
20	chr7:120468600-120487600	Weak transcription	Lung	lung
21	chr7:120468800-120476000	Weak transcription	Aorta	Aorta
22	chr7:120469800-120476000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr7:120470000-120476200	Weak transcription	Liver	Liver
24	chr7:120470600-120484600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:120471800-120475600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:120471800-120479800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:120472000-120479600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr7:120472200-120474600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:120472200-120475200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr7:120472400-120475800	Weak transcription	Fetal Kidney	kidney
31	chr7:120472400-120476200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:120472600-120475600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:120472600-120476000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:120472600-120479800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:120473400-120474600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr7:120473800-120476600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr7:120473800-120482000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:120474000-120474600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr7:120474000-120474800	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr7:120474000-120475200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr7:120474000-120476000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:120474000-120476000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr7:120474000-120476400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr7:120474000-120477200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr7:120474000-120480000	Weak transcription	HSMMtube	muscle
46	chr7:120474000-120482000	Weak transcription	Colon Smooth Muscle	Colon
47	chr7:120474000-120482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:120474000-120482200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:120474000-120492400	Weak transcription	Fetal Lung	lung
50	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach

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