Variant report

Variant	rs17725024
Chromosome Location	chr2:72498920-72498921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72464976..72467489-chr2:72497320..72499633,2	MCF-7	breast:
2	chr2:72494142..72496291-chr2:72497712..72499384,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1000523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1003672	0.92[ASN][1000 genomes]
rs10175915	1.00[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];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178847	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181899	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193543	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10204415	0.87[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10205108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10209861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10221767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221769	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10865390	0.92[ASN][1000 genomes]
rs11126362	0.85[ASN][1000 genomes]
rs11126363	0.92[ASN][1000 genomes]
rs1123199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1159763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11675268	1.00[JPT][hapmap]
rs11681809	0.92[ASN][1000 genomes]
rs12463825	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12466026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12466112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382986	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387630	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391463	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13392314	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13404369	0.92[ASN][1000 genomes]
rs13409641	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13417114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs13418637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13423761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13430254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430651	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432350	0.91[GIH][hapmap]
rs17008208	1.00[JPT][hapmap]
rs17673916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724860	1.00[ASW][hapmap];1.00[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];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs194237	0.92[ASN][1000 genomes]
rs194238	0.92[ASN][1000 genomes]
rs194241	0.92[ASN][1000 genomes]
rs194242	0.85[ASN][1000 genomes]
rs194243	0.85[ASN][1000 genomes]
rs2041563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2041564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2080044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109960	0.86[CEU][hapmap]
rs2109963	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2159823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192015	0.80[GIH][hapmap]
rs28278	0.85[ASN][1000 genomes]
rs41386	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs41387	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs41388	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[ASN][1000 genomes]
rs41389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[ASN][1000 genomes]
rs41390	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41391	0.85[ASN][1000 genomes]
rs41392	1.00[CHB][hapmap]
rs41393	1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[ASN][1000 genomes]
rs41394	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[ASN][1000 genomes]
rs41396	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41398	1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[ASN][1000 genomes]
rs41399	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs41400	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41401	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41403	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[ASN][1000 genomes]
rs41405	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41406	1.00[CHB][hapmap]
rs41407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[ASN][1000 genomes]
rs41408	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41409	0.85[ASN][1000 genomes]
rs41412	0.91[GIH][hapmap]
rs41415	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs41416	0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs41417	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs41420	0.85[ASN][1000 genomes]
rs4852285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4852286	0.91[GIH][hapmap];1.00[MEX][hapmap]
rs4852288	0.91[GIH][hapmap]
rs4852859	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852860	0.92[ASN][1000 genomes]
rs4852861	0.85[ASN][1000 genomes]
rs4852862	0.92[ASN][1000 genomes]
rs55764675	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55877105	0.85[ASN][1000 genomes]
rs55970539	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56045434	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56143801	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56299443	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147573	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147579	0.85[ASN][1000 genomes]
rs62147589	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147626	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147629	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147636	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149273	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs636734	1.00[ASW][hapmap]
rs6546752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6546753	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6546755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6711257	0.82[EUR][1000 genomes]
rs6719255	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6751276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6760895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs719117	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7559131	0.91[GIH][hapmap]
rs7565922	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7583271	0.91[GIH][hapmap]
rs768042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs768043	0.85[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17725024	CCT7	cis	parietal	SCAN
rs17725024	BOLA3	cis	parietal	SCAN
rs17725024	FBXO48	cis	cerebellum	SCAN
rs17725024	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72485200-72501800	Weak transcription	HSMMtube	muscle
2	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
3	chr2:72491200-72502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:72496400-72500000	Enhancers	Fetal Heart	heart
5	chr2:72497200-72503400	Enhancers	Fetal Intestine Large	intestine
6	chr2:72497400-72499000	Weak transcription	Right Ventricle	heart
7	chr2:72497400-72499200	Weak transcription	Right Atrium	heart
8	chr2:72497400-72500600	Weak transcription	Pancreas	Pancrea
9	chr2:72497400-72505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:72497600-72499000	Weak transcription	Left Ventricle	heart
11	chr2:72498000-72499800	Enhancers	Brain Anterior Caudate	brain
12	chr2:72498000-72500000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:72498000-72503000	Enhancers	Fetal Intestine Small	intestine
14	chr2:72498200-72499600	Enhancers	Colon Smooth Muscle	Colon
15	chr2:72498200-72499600	Enhancers	Small Intestine	intestine
16	chr2:72498200-72499800	Enhancers	Brain Hippocampus Middle	brain
17	chr2:72498200-72500200	Enhancers	Fetal Kidney	kidney
18	chr2:72498200-72501600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:72498200-72502400	Flanking Active TSS	A549	lung
20	chr2:72498400-72499000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr2:72498400-72499400	Enhancers	Esophagus	oesophagus
22	chr2:72498400-72499400	Enhancers	Psoas Muscle	Psoas
23	chr2:72498400-72499400	Enhancers	Thymus	Thymus
24	chr2:72498400-72499600	Enhancers	Brain Angular Gyrus	brain
25	chr2:72498400-72499600	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:72498400-72499800	Enhancers	Fetal Lung	lung
27	chr2:72498400-72501000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:72498400-72502800	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:72498600-72499000	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:72498600-72499200	Weak transcription	Stomach Mucosa	stomach
31	chr2:72498600-72499400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:72498600-72499400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:72498600-72499400	Enhancers	Hela-S3	cervix
34	chr2:72498600-72499600	Enhancers	Brain Germinal Matrix	brain
35	chr2:72498600-72499800	Enhancers	Brain Substantia Nigra	brain
36	chr2:72498600-72499800	Enhancers	Ovary	ovary
37	chr2:72498600-72499800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr2:72498800-72499400	Enhancers	HUVEC	blood vessel
39	chr2:72498800-72499600	Enhancers	Adipose Nuclei	Adipose
40	chr2:72498800-72499800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:72498800-72499800	Enhancers	Liver	Liver
42	chr2:72498800-72499800	Enhancers	Fetal Stomach	stomach

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