Variant report

Variant	rs41416
Chromosome Location	chr2:72405008-72405009
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:72333139..72335001-chr2:72404125..72406066,2	K562	blood:
2	chr1:41733579..41734213-chr2:72404592..72405273,2	MCF-7	breast:
3	chr2:72403994..72406208-chr2:72407715..72409374,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYSF-12	chr2:72402989-72405839	NONHSAT071575

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1000523	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs10175915	0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs10178138	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs10178847	0.85[ASN][1000 genomes]
rs10181899	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs10190799	0.80[ASN][1000 genomes]
rs10193543	0.85[ASN][1000 genomes]
rs10204415	0.91[GIH][hapmap];0.81[MEX][hapmap]
rs10205108	0.91[GIH][hapmap]
rs10221767	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs10221769	0.91[GIH][hapmap]
rs10865390	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11126362	0.86[ASN][1000 genomes]
rs1123199	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs1159764	0.91[GIH][hapmap]
rs1159766	0.91[GIH][hapmap]
rs11681809	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12466026	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs12466112	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs13382986	0.85[ASN][1000 genomes]
rs13387630	0.85[ASN][1000 genomes]
rs13389524	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs13392314	0.85[ASN][1000 genomes]
rs13409641	0.81[CEU][hapmap]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13417114	0.87[GIH][hapmap]
rs13430254	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs13430651	0.85[ASN][1000 genomes]
rs13432350	0.87[GIH][hapmap]
rs17673916	0.87[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs17724205	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs17724860	0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs17725024	0.87[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs194235	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs194237	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194238	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194241	0.81[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	0.83[GIH][hapmap]
rs2080044	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs2109963	0.83[GIH][hapmap]
rs2159823	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs28278	0.86[ASN][1000 genomes]
rs41386	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs41387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41388	0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41389	0.91[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];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41394	0.91[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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41399	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41400	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41401	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41402	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41403	0.91[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	0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41408	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41409	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41414	0.93[ASN][1000 genomes]
rs41415	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41417	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]
rs41418	0.93[ASN][1000 genomes]
rs41419	0.93[ASN][1000 genomes]
rs41420	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852286	0.87[GIH][hapmap];0.93[MEX][hapmap]
rs4852288	0.87[GIH][hapmap]
rs4852859	0.85[ASN][1000 genomes]
rs55764675	0.85[ASN][1000 genomes]
rs55970539	0.85[ASN][1000 genomes]
rs56299443	0.85[ASN][1000 genomes]
rs62147573	0.85[ASN][1000 genomes]
rs62147589	0.85[ASN][1000 genomes]
rs62147626	0.85[ASN][1000 genomes]
rs62147629	0.85[ASN][1000 genomes]
rs62147636	0.85[ASN][1000 genomes]
rs6546753	0.83[GIH][hapmap]
rs6719255	0.85[ASN][1000 genomes]
rs6760895	0.83[GIH][hapmap]
rs7559131	0.87[GIH][hapmap]
rs7565922	0.83[GIH][hapmap]
rs7583271	0.87[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
rs41416	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:93 , 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	chr2:72394400-72409800	Weak transcription	A549	lung
4	chr2:72398400-72407400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:72399600-72405800	Weak transcription	Esophagus	oesophagus
6	chr2:72400600-72405600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:72400600-72406400	Weak transcription	Fetal Brain Male	brain
8	chr2:72400800-72414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:72401000-72405600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:72401000-72407000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:72401000-72407800	Strong transcription	Fetal Stomach	stomach
12	chr2:72401200-72406000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:72401200-72406000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:72401200-72407600	Strong transcription	Fetal Brain Female	brain
15	chr2:72401200-72409600	Weak transcription	Spleen	Spleen
16	chr2:72401400-72409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:72401600-72407200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:72401600-72409400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:72401600-72411600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:72401600-72414000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:72401600-72415200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:72401800-72405200	Weak transcription	NH-A	brain
23	chr2:72401800-72407000	Strong transcription	Brain Hippocampus Middle	brain
24	chr2:72401800-72407600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:72401800-72407600	Strong transcription	Left Ventricle	heart
26	chr2:72402000-72405400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:72402000-72406200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:72402000-72406400	Strong transcription	Brain Anterior Caudate	brain
29	chr2:72402000-72410400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:72402200-72405800	Strong transcription	Brain Angular Gyrus	brain
31	chr2:72402200-72406400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:72402200-72406600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:72402200-72406600	Strong transcription	Placenta	Placenta
34	chr2:72402200-72406800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:72402200-72410400	Weak transcription	Psoas Muscle	Psoas
36	chr2:72402200-72412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:72402400-72405800	Weak transcription	Fetal Heart	heart
38	chr2:72402400-72406400	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:72402400-72406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:72402400-72407200	Strong transcription	Adipose Nuclei	Adipose
41	chr2:72402400-72407400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:72402600-72405400	Strong transcription	Pancreas	Pancrea
43	chr2:72402600-72406400	Strong transcription	Primary T cells from cord blood	blood
44	chr2:72402600-72407200	Strong transcription	Aorta	Aorta
45	chr2:72402600-72407400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:72402600-72410400	Weak transcription	Small Intestine	intestine
47	chr2:72402800-72407000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:72403000-72405600	Strong transcription	HSMMtube	muscle
49	chr2:72403000-72406400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:72403000-72408800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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