Variant report

Variant	rs41413
Chromosome Location	chr2:72405833-72405834
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	chr2:72333139..72335001-chr2:72404125..72406066,2	K562	blood:
2	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: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003672	0.81[ASN][1000 genomes]
rs10190799	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10196589	0.81[ASN][1000 genomes]
rs10205108	0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs10209861	0.87[ASN][1000 genomes]
rs10221769	0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs10865390	0.81[ASN][1000 genomes]
rs11126362	0.87[ASN][1000 genomes]
rs11126363	0.81[ASN][1000 genomes]
rs1159763	0.81[ASN][1000 genomes]
rs1159764	0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs1159765	0.81[ASN][1000 genomes]
rs1159766	0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs11681809	0.81[ASN][1000 genomes]
rs13391463	0.84[CEU][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13395204	0.87[ASN][1000 genomes]
rs13404369	0.81[ASN][1000 genomes]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13417114	0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs13418637	0.81[ASN][1000 genomes]
rs13423761	0.87[CEU][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194235	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs194237	0.81[ASN][1000 genomes]
rs194238	0.81[ASN][1000 genomes]
rs194239	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs194241	0.81[ASN][1000 genomes]
rs194242	0.87[ASN][1000 genomes]
rs194243	0.87[ASN][1000 genomes]
rs2041563	0.91[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs2041564	0.87[ASN][1000 genomes]
rs2109963	0.91[GIH][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs2192015	0.84[GIH][hapmap]
rs28278	0.87[ASN][1000 genomes]
rs41386	1.00[JPT][hapmap]
rs41387	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41388	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41389	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41390	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41391	0.87[ASN][1000 genomes]
rs41392	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41393	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41394	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41396	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41398	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41399	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41400	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41401	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41402	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41403	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41405	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41406	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41407	0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41408	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41411	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41412	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	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs41415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41416	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41417	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41418	0.94[ASN][1000 genomes]
rs41419	0.94[ASN][1000 genomes]
rs41420	0.87[ASN][1000 genomes]
rs4852285	0.83[CEU][hapmap];0.87[ASN][1000 genomes]
rs4852860	0.81[ASN][1000 genomes]
rs4852861	0.87[ASN][1000 genomes]
rs4852862	0.81[ASN][1000 genomes]
rs55877105	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62147579	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546752	0.81[ASN][1000 genomes]
rs6546753	0.91[GIH][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs6546755	0.87[ASN][1000 genomes]
rs6748607	0.87[ASN][1000 genomes]
rs6751276	0.87[ASN][1000 genomes]
rs6760895	0.91[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs7565922	0.87[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs768042	0.87[ASN][1000 genomes]
rs768043	0.87[ASN][1000 genomes]
rs9309463	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41413	MOGS	cis	cerebellum	SCAN
rs41413	PNO1	cis	parietal	SCAN
rs41413	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:94 , 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	chr2:72400600-72406400	Weak transcription	Fetal Brain Male	brain
6	chr2:72400800-72414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:72401000-72407000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:72401000-72407800	Strong transcription	Fetal Stomach	stomach
9	chr2:72401200-72406000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:72401200-72406000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:72401200-72407600	Strong transcription	Fetal Brain Female	brain
12	chr2:72401200-72409600	Weak transcription	Spleen	Spleen
13	chr2:72401400-72409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:72401600-72407200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:72401600-72409400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:72401600-72411600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:72401600-72414000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:72401600-72415200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:72401800-72407000	Strong transcription	Brain Hippocampus Middle	brain
20	chr2:72401800-72407600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:72401800-72407600	Strong transcription	Left Ventricle	heart
22	chr2:72402000-72406200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:72402000-72406400	Strong transcription	Brain Anterior Caudate	brain
24	chr2:72402000-72410400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:72402200-72406400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:72402200-72406600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:72402200-72406600	Strong transcription	Placenta	Placenta
28	chr2:72402200-72406800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:72402200-72410400	Weak transcription	Psoas Muscle	Psoas
30	chr2:72402200-72412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:72402400-72406400	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:72402400-72406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:72402400-72407200	Strong transcription	Adipose Nuclei	Adipose
34	chr2:72402400-72407400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:72402600-72406400	Strong transcription	Primary T cells from cord blood	blood
36	chr2:72402600-72407200	Strong transcription	Aorta	Aorta
37	chr2:72402600-72407400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:72402600-72410400	Weak transcription	Small Intestine	intestine
39	chr2:72402800-72407000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:72403000-72406400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:72403000-72408800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:72403000-72410200	Weak transcription	Fetal Kidney	kidney
43	chr2:72403200-72408000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:72403200-72408800	Weak transcription	Colonic Mucosa	Colon
45	chr2:72403400-72406400	Strong transcription	Fetal Intestine Large	intestine
46	chr2:72403400-72406600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:72403400-72406600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr2:72403400-72409000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:72403400-72414200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:72403600-72406800	Weak transcription	Primary T cells fromperipheralblood	blood

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