Variant report

Variant	rs41412
Chromosome Location	chr2:72407263-72407264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1003672	0.86[ASN][1000 genomes]
rs10175915	0.91[GIH][hapmap]
rs10190799	0.87[ASN][1000 genomes]
rs10196589	0.86[ASN][1000 genomes]
rs10204415	0.87[GIH][hapmap]
rs10205108	0.95[GIH][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs10209861	0.80[ASN][1000 genomes]
rs10221769	0.95[GIH][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs10865390	0.86[ASN][1000 genomes]
rs11126362	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11126363	0.86[ASN][1000 genomes]
rs1159763	0.86[ASN][1000 genomes]
rs1159764	0.95[GIH][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs1159765	0.86[ASN][1000 genomes]
rs1159766	0.95[GIH][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs11681809	0.86[ASN][1000 genomes]
rs13391463	0.80[ASN][1000 genomes]
rs13395204	0.80[ASN][1000 genomes]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13417114	0.83[GIH][hapmap]
rs13418637	0.86[ASN][1000 genomes]
rs13423761	0.80[ASN][1000 genomes]
rs13432350	0.91[GIH][hapmap]
rs17673916	0.87[GIH][hapmap]
rs17724860	0.91[GIH][hapmap]
rs17725024	0.91[GIH][hapmap]
rs194235	0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs194236	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs194237	0.86[ASN][1000 genomes]
rs194238	0.86[ASN][1000 genomes]
rs194240	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs194241	0.86[ASN][1000 genomes]
rs194242	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194243	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041563	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs2041564	0.80[ASN][1000 genomes]
rs2109963	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs28278	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41386	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs41387	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41388	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41389	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41390	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41391	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41392	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41394	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41396	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41399	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41400	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41401	0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41402	0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs41403	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41406	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41407	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41408	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs41411	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs41413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs41414	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41416	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41417	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41418	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41419	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41420	0.93[ASN][1000 genomes]
rs4852285	0.80[ASN][1000 genomes]
rs4852286	0.83[GIH][hapmap]
rs4852288	0.91[GIH][hapmap]
rs4852861	0.80[ASN][1000 genomes]
rs55877105	0.80[ASN][1000 genomes]
rs62147579	0.80[ASN][1000 genomes]
rs6546752	0.86[ASN][1000 genomes]
rs6546753	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs6546755	0.80[ASN][1000 genomes]
rs6748607	0.80[ASN][1000 genomes]
rs6751276	0.80[ASN][1000 genomes]
rs6760895	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs7559131	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs7565922	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs7583271	0.91[GIH][hapmap]
rs768042	0.80[ASN][1000 genomes]
rs768043	0.80[ASN][1000 genomes]
rs9309463	0.86[ASN][1000 genomes]

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
rs41412	C20orf24	trans	cerebellum	SCAN

Chromatin state (count:88 , 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	chr2:72400800-72414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:72401000-72407800	Strong transcription	Fetal Stomach	stomach
7	chr2:72401200-72407600	Strong transcription	Fetal Brain Female	brain
8	chr2:72401200-72409600	Weak transcription	Spleen	Spleen
9	chr2:72401400-72409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:72401600-72409400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:72401600-72411600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:72401600-72414000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:72401600-72415200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:72401800-72407600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:72401800-72407600	Strong transcription	Left Ventricle	heart
16	chr2:72402000-72410400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:72402200-72410400	Weak transcription	Psoas Muscle	Psoas
18	chr2:72402200-72412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:72402400-72407400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:72402600-72407400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:72402600-72410400	Weak transcription	Small Intestine	intestine
22	chr2:72403000-72408800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:72403000-72410200	Weak transcription	Fetal Kidney	kidney
24	chr2:72403200-72408000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:72403200-72408800	Weak transcription	Colonic Mucosa	Colon
26	chr2:72403400-72409000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:72403400-72414200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:72404000-72408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:72404600-72407600	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr2:72405200-72408000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:72405400-72409600	Weak transcription	Pancreas	Pancrea
32	chr2:72405400-72414000	Weak transcription	Fetal Intestine Small	intestine
33	chr2:72405600-72411200	Weak transcription	HSMMtube	muscle
34	chr2:72405600-72414000	Weak transcription	Lung	lung
35	chr2:72405800-72409000	Weak transcription	Stomach Mucosa	stomach
36	chr2:72405800-72418600	Weak transcription	Brain Angular Gyrus	brain
37	chr2:72406000-72407600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:72406000-72407600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:72406000-72407800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:72406000-72407800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:72406000-72412400	Weak transcription	Liver	Liver
42	chr2:72406200-72407800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:72406200-72408000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:72406200-72409800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:72406200-72412200	Weak transcription	Fetal Heart	heart
46	chr2:72406400-72408000	Weak transcription	Primary T cells from cord blood	blood
47	chr2:72406400-72408200	Weak transcription	HepG2	liver
48	chr2:72406400-72408400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:72406400-72408400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:72406400-72408600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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