Variant report

Variant	rs41420
Chromosome Location	chr2:72402254-72402255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1000523	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs10175915	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs10178138	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs10178847	0.85[ASN][1000 genomes]
rs10181899	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs10190799	0.80[ASN][1000 genomes]
rs10193543	0.85[ASN][1000 genomes]
rs10204415	0.95[GIH][hapmap];0.81[MEX][hapmap]
rs10205108	0.95[GIH][hapmap]
rs10221767	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs10221769	0.95[GIH][hapmap]
rs10865390	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11126362	0.86[ASN][1000 genomes]
rs1123199	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs1159764	0.95[GIH][hapmap]
rs1159766	0.95[GIH][hapmap]
rs11681809	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12466026	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12466112	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13382986	0.85[ASN][1000 genomes]
rs13387630	0.85[ASN][1000 genomes]
rs13389524	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs13392314	0.85[ASN][1000 genomes]
rs13409641	0.82[CEU][hapmap]
rs13410366	1.00[YRI][hapmap]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13417114	0.91[GIH][hapmap]
rs13430254	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs13430651	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13432350	0.91[GIH][hapmap]
rs17673916	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]
rs17724205	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17724860	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs17725024	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]
rs194235	0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs194237	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194238	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194241	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194242	0.86[ASN][1000 genomes]
rs194243	0.86[ASN][1000 genomes]
rs2041563	0.87[GIH][hapmap]
rs2080044	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2109963	0.87[GIH][hapmap]
rs2159823	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2192015	0.80[GIH][hapmap]
rs28278	0.86[ASN][1000 genomes]
rs41386	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs41387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41388	0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41389	0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41390	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41391	0.86[ASN][1000 genomes]
rs41392	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41393	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41394	0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41396	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41398	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41399	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41400	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41401	0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41402	0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41403	0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41406	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41407	0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41408	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41409	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41411	0.87[ASN][1000 genomes]
rs41412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41413	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41414	0.93[ASN][1000 genomes]
rs41415	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];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41417	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[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41418	0.93[ASN][1000 genomes]
rs41419	0.93[ASN][1000 genomes]
rs4852286	0.91[GIH][hapmap];0.93[MEX][hapmap]
rs4852288	0.91[GIH][hapmap]
rs4852859	0.85[ASN][1000 genomes]
rs55764675	0.85[ASN][1000 genomes]
rs55970539	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56299443	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62147573	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62147589	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62147626	0.85[ASN][1000 genomes]
rs62147629	0.85[ASN][1000 genomes]
rs62147636	0.85[ASN][1000 genomes]
rs6546753	0.87[GIH][hapmap]
rs6719255	0.85[ASN][1000 genomes]
rs6760895	0.87[GIH][hapmap]
rs7559131	0.91[GIH][hapmap]
rs7565922	0.87[GIH][hapmap]
rs7583271	0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41420	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72393400-72407600	Weak transcription	HMEC	breast
2	chr2:72393600-72414800	Weak transcription	NHEK	skin
3	chr2:72394400-72402600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:72394400-72403000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:72394400-72409800	Weak transcription	A549	lung
6	chr2:72395000-72402400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:72397200-72403400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:72398400-72407400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:72399600-72403600	Weak transcription	Brain Germinal Matrix	brain
10	chr2:72399600-72405800	Weak transcription	Esophagus	oesophagus
11	chr2:72400000-72403000	Weak transcription	HSMMtube	muscle
12	chr2:72400000-72403400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:72400000-72404400	Weak transcription	Liver	Liver
14	chr2:72400200-72402600	Weak transcription	Primary T cells from cord blood	blood
15	chr2:72400400-72402600	Weak transcription	Aorta	Aorta
16	chr2:72400600-72404600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:72400600-72405600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:72400600-72406400	Weak transcription	Fetal Brain Male	brain
19	chr2:72400800-72414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:72401000-72402800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:72401000-72404600	Weak transcription	Gastric	stomach
22	chr2:72401000-72404600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:72401000-72405600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:72401000-72407000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:72401000-72407800	Strong transcription	Fetal Stomach	stomach
26	chr2:72401200-72402400	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:72401200-72402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:72401200-72402600	Weak transcription	Pancreas	Pancrea
29	chr2:72401200-72403000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:72401200-72403400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:72401200-72403600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:72401200-72403800	Weak transcription	Brain Substantia Nigra	brain
33	chr2:72401200-72403800	Weak transcription	Right Ventricle	heart
34	chr2:72401200-72403800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:72401200-72404600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:72401200-72404600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:72401200-72404800	Weak transcription	Ovary	ovary
38	chr2:72401200-72405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:72401200-72406000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:72401200-72406000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:72401200-72407600	Strong transcription	Fetal Brain Female	brain
42	chr2:72401200-72409600	Weak transcription	Spleen	Spleen
43	chr2:72401400-72402400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:72401400-72402800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:72401400-72404200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:72401400-72409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:72401600-72402400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:72401600-72404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:72401600-72404800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:72401600-72405000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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