Variant report

Variant	rs13409641
Chromosome Location	chr2:72501773-72501774
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	chr2:72496641..72498799-chr2:72499745..72502652,2	K562	blood:

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1000523	0.94[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10168145	1.00[CHB][hapmap]
rs10173381	1.00[CHB][hapmap]
rs10175915	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10178138	0.94[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10178847	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10181899	0.94[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10186080	1.00[CHB][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap]
rs10193543	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10203965	1.00[CHB][hapmap]
rs10204415	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207299	1.00[CHB][hapmap]
rs10221767	0.94[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11126366	1.00[CHB][hapmap]
rs1123199	0.94[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11690734	1.00[CHB][hapmap]
rs11694921	1.00[CHB][hapmap]
rs11902025	1.00[CHB][hapmap]
rs12463825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12466026	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12466112	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12466613	1.00[CHB][hapmap]
rs12467816	1.00[CHB][hapmap]
rs12468057	1.00[CHB][hapmap]
rs12471875	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs13382986	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13383535	1.00[CHB][hapmap]
rs13387630	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13389524	0.94[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13390754	1.00[CHB][hapmap]
rs13392314	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13409513	1.00[CHB][hapmap]
rs13430254	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs13430651	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13432350	1.00[CHB][hapmap]
rs1400582	1.00[CHB][hapmap]
rs1568145	1.00[CHB][hapmap]
rs17673916	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17724205	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17724860	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17725024	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2080044	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2109960	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs2159823	0.94[CEU][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2192014	1.00[CHB][hapmap]
rs2192015	1.00[CHB][hapmap]
rs2203679	1.00[CHB][hapmap]
rs2420444	1.00[CHB][hapmap]
rs2901146	1.00[CHB][hapmap]
rs3115351	1.00[CHB][hapmap]
rs41386	0.82[CEU][hapmap]
rs41387	0.83[CEU][hapmap]
rs41399	0.83[CEU][hapmap]
rs41408	0.81[CEU][hapmap]
rs41409	0.80[CEU][hapmap]
rs41415	0.82[CEU][hapmap]
rs41416	0.81[CEU][hapmap]
rs41417	0.82[CEU][hapmap]
rs4852286	1.00[CHB][hapmap]
rs4852287	1.00[CHB][hapmap]
rs4852288	1.00[CHB][hapmap]
rs4852859	0.92[EUR][1000 genomes]
rs55764675	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55970539	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56045434	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56143801	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56299443	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs585653	1.00[CHB][hapmap]
rs587431	1.00[CHB][hapmap]
rs587744	1.00[CHB][hapmap]
rs589547	1.00[CHB][hapmap]
rs590252	1.00[CHB][hapmap]
rs590345	1.00[CHB][hapmap]
rs598138	1.00[CHB][hapmap]
rs598496	1.00[CHB][hapmap]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap]
rs614653	1.00[CHB][hapmap]
rs62147573	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62147589	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62147626	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62147629	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62147636	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62149273	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CHB][hapmap]
rs630241	1.00[CHB][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634785	1.00[CHB][hapmap]
rs634929	1.00[CHB][hapmap]
rs636319	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap]
rs638854	1.00[CHB][hapmap]
rs640610	1.00[CHB][hapmap]
rs641123	1.00[CHB][hapmap]
rs641939	1.00[CHB][hapmap]
rs642652	1.00[CHB][hapmap]
rs647242	1.00[CHB][hapmap]
rs647269	1.00[CHB][hapmap]
rs6546756	1.00[CHB][hapmap]
rs6546760	1.00[CHB][hapmap]
rs6546764	1.00[CHB][hapmap]
rs6546765	1.00[CHB][hapmap]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CHB][hapmap]
rs663218	1.00[CHB][hapmap]
rs666233	1.00[CHB][hapmap]
rs666361	1.00[CHB][hapmap]
rs669074	1.00[CHB][hapmap]
rs6709114	1.00[ASN][1000 genomes]
rs6711257	0.87[EUR][1000 genomes]
rs6719255	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6729863	1.00[CHB][hapmap]
rs6733210	1.00[CHB][hapmap]
rs6742264	1.00[CHB][hapmap]
rs674863	1.00[CHB][hapmap]
rs6752122	1.00[CHB][hapmap]
rs6753073	1.00[CHB][hapmap]
rs6758462	1.00[CHB][hapmap]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CHB][hapmap]
rs681574	1.00[CHB][hapmap]
rs687325	1.00[CHB][hapmap]
rs687371	1.00[CHB][hapmap]
rs688433	1.00[CHB][hapmap]
rs689154	1.00[CHB][hapmap]
rs719117	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558686	1.00[CHB][hapmap]
rs7558919	1.00[CHB][hapmap]
rs7559131	1.00[CHB][hapmap]
rs7568803	1.00[CHB][hapmap]
rs7577877	1.00[CHB][hapmap]
rs7583271	1.00[CHB][hapmap]
rs7594350	1.00[CHB][hapmap]
rs7595180	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs9309464	1.00[CHB][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13409641	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:39 , 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	chr2:72497200-72503400	Enhancers	Fetal Intestine Large	intestine
5	chr2:72497400-72505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:72498000-72503000	Enhancers	Fetal Intestine Small	intestine
7	chr2:72498200-72502400	Flanking Active TSS	A549	lung
8	chr2:72498400-72502800	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:72499000-72502400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:72499400-72502200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:72499400-72503000	Weak transcription	Left Ventricle	heart
12	chr2:72499400-72507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:72499400-72507800	Weak transcription	Psoas Muscle	Psoas
14	chr2:72499600-72501800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:72499600-72501800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:72499600-72502200	Weak transcription	Small Intestine	intestine
17	chr2:72499600-72502800	Weak transcription	Right Atrium	heart
18	chr2:72499600-72510400	Weak transcription	Right Ventricle	heart
19	chr2:72499800-72501800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:72499800-72502000	Weak transcription	Fetal Brain Male	brain
21	chr2:72499800-72502400	Weak transcription	Ovary	ovary
22	chr2:72499800-72505200	Weak transcription	NHEK	skin
23	chr2:72500200-72502000	Weak transcription	Fetal Kidney	kidney
24	chr2:72500400-72501800	Enhancers	Stomach Mucosa	stomach
25	chr2:72500400-72502200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:72500600-72502800	Enhancers	Hela-S3	cervix
27	chr2:72500600-72503600	Enhancers	Brain Substantia Nigra	brain
28	chr2:72501000-72502600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr2:72501000-72503000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:72501000-72505800	Weak transcription	Pancreas	Pancrea
31	chr2:72501400-72501800	Enhancers	Liver	Liver
32	chr2:72501400-72502000	Enhancers	Fetal Lung	lung
33	chr2:72501400-72502800	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:72501600-72501800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr2:72501600-72502000	Enhancers	Colon Smooth Muscle	Colon
36	chr2:72501600-72502200	Enhancers	Brain Anterior Caudate	brain
37	chr2:72501600-72503400	Enhancers	Fetal Heart	heart
38	chr2:72501600-72503400	Weak transcription	NH-A	brain
39	chr2:72501600-72503600	Enhancers	Brain Hippocampus Middle	brain

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