Variant report

Variant	rs6466421
Chromosome Location	chr7:112427102-112427103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112421571..112428519-chr7:112428661..112431818,11	MCF-7	breast:
2	chr1:149856779..149859467-chr7:112424877..112427424,2	MCF-7	breast:
3	chr7:112421681..112427261-chr7:112427948..112432124,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000146802	Chromatin interaction
ENSG00000184678	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10216223	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10238492	0.82[CHB][hapmap]
rs10247759	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10249701	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10269793	0.90[ASN][1000 genomes]
rs10271752	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10273589	0.82[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs10275208	0.82[CHB][hapmap]
rs10280638	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1227155	0.90[ASN][1000 genomes]
rs1227158	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1227159	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1227163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1227168	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227171	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1227172	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227174	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227176	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227177	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1227178	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1227181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1227183	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1227190	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238698	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535487	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs12539085	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1530756	0.82[CHB][hapmap]
rs1547554	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1615468	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17160078	0.82[CHB][hapmap]
rs1718944	1.00[JPT][hapmap]
rs1718955	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718957	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718961	0.81[ASN][1000 genomes]
rs1718967	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1718969	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1796491	0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796492	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796493	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796512	0.81[ASN][1000 genomes]
rs1796516	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922907	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1996843	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2028028	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2396570	0.82[CHB][hapmap]
rs2396574	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2457	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687267	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2708295	0.81[ASN][1000 genomes]
rs2708296	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3957315	0.82[CHB][hapmap]
rs3997335	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs494324	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs548994	0.90[CEU][hapmap]
rs549688	0.86[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs552304	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs564494	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs660743	0.85[JPT][hapmap]
rs672911	1.00[JPT][hapmap]
rs685259	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6944843	0.82[CHB][hapmap]
rs6945635	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6946335	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6948575	0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs6948876	0.90[ASN][1000 genomes]
rs6953522	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6955834	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970266	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs726593	0.91[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7777973	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7778135	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7781871	0.82[CHB][hapmap]
rs7789772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803405	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806781	1.00[CHB][hapmap]
rs7808616	0.82[CHB][hapmap]
rs821783	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs821785	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs821787	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs9649356	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9655816	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9969347	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv2752144	chr7:112398372-112499924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6466421	CAV2	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112393600-112429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:112396200-112428600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:112397000-112428000	Weak transcription	Fetal Intestine Small	intestine
4	chr7:112397600-112429600	Weak transcription	Pancreas	Pancrea
5	chr7:112398800-112428800	Weak transcription	Gastric	stomach
6	chr7:112400200-112429000	Weak transcription	HSMM	muscle
7	chr7:112400600-112428600	Weak transcription	Brain Substantia Nigra	brain
8	chr7:112403400-112428600	Weak transcription	Fetal Stomach	stomach
9	chr7:112404800-112428800	Weak transcription	Spleen	Spleen
10	chr7:112405400-112428400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:112405600-112428800	Weak transcription	Osteobl	bone
12	chr7:112405800-112428200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:112405800-112428800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:112406000-112428800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:112406000-112429000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:112406400-112428800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:112406400-112429000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:112406600-112428400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:112407800-112428600	Weak transcription	Ovary	ovary
20	chr7:112410600-112428600	Weak transcription	Fetal Lung	lung
21	chr7:112410600-112428600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:112411400-112428400	Weak transcription	Brain Anterior Caudate	brain
23	chr7:112411600-112428600	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:112411800-112428800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:112413000-112428600	Weak transcription	Fetal Kidney	kidney
26	chr7:112413200-112429000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:112413800-112429000	Weak transcription	Esophagus	oesophagus
28	chr7:112418400-112428400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr7:112418400-112428600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:112418600-112429000	Weak transcription	Placenta	Placenta
31	chr7:112419400-112429200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:112419600-112428600	Weak transcription	Fetal Brain Female	brain
33	chr7:112419800-112428600	Weak transcription	NHLF	lung
34	chr7:112421600-112428200	Weak transcription	Dnd41	blood
35	chr7:112421600-112428400	Weak transcription	Brain Hippocampus Middle	brain
36	chr7:112421600-112428400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr7:112421600-112428800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:112422000-112428400	Weak transcription	Stomach Mucosa	stomach
39	chr7:112422200-112428600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:112422800-112428200	Weak transcription	Fetal Heart	heart
41	chr7:112422800-112428600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr7:112422800-112429000	Weak transcription	Psoas Muscle	Psoas
43	chr7:112422800-112429200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:112422800-112429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:112423000-112428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:112423000-112428800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:112423000-112428800	Weak transcription	Aorta	Aorta
48	chr7:112423000-112429000	Weak transcription	HSMMtube	muscle
49	chr7:112423000-112429800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:112423200-112428400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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