Variant report

Variant	rs41401
Chromosome Location	chr2:72419303-72419304
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	chr2:72417923..72420576-chr2:72426721..72428374,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1000523	1.00[CHB][hapmap]
rs1003672	0.86[ASN][1000 genomes]
rs10175915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs10178138	1.00[CHB][hapmap]
rs10190799	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10204415	0.83[GIH][hapmap]
rs10205108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs10209861	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs10221767	1.00[CHB][hapmap]
rs10221769	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs10865390	0.86[ASN][1000 genomes]
rs11126362	0.93[ASN][1000 genomes]
rs11126363	0.86[ASN][1000 genomes]
rs1123199	1.00[CHB][hapmap]
rs1159763	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs11681809	0.86[ASN][1000 genomes]
rs12466026	1.00[CHB][hapmap]
rs12466112	1.00[CHB][hapmap]
rs13389524	1.00[CHB][hapmap]
rs13391463	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13395204	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs13404369	0.86[ASN][1000 genomes]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13417114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[ASN][1000 genomes]
rs13418637	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13423761	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430254	1.00[CHB][hapmap]
rs13432350	0.87[GIH][hapmap]
rs17673916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs17724205	1.00[CHB][hapmap]
rs17724860	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs17725024	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs194235	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194236	0.81[ASN][1000 genomes]
rs194237	0.86[ASN][1000 genomes]
rs194238	0.86[ASN][1000 genomes]
rs194239	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs194240	0.81[ASN][1000 genomes]
rs194241	0.86[ASN][1000 genomes]
rs194242	0.93[ASN][1000 genomes]
rs194243	0.93[ASN][1000 genomes]
rs2041563	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs2041564	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2080044	1.00[CHB][hapmap]
rs2109963	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs2159823	1.00[CHB][hapmap]
rs2192015	0.92[GIH][hapmap]
rs28278	0.93[ASN][1000 genomes]
rs41386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs41387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41388	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41391	0.93[ASN][1000 genomes]
rs41392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41393	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41394	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41395	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41397	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41398	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41402	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];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41403	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41405	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41409	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41410	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41411	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41412	0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41413	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]
rs41414	0.87[ASN][1000 genomes]
rs41415	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41416	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41417	0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs41418	0.87[ASN][1000 genomes]
rs41419	0.87[ASN][1000 genomes]
rs41420	0.80[ASN][1000 genomes]
rs4852285	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4852288	0.87[GIH][hapmap]
rs4852860	0.86[ASN][1000 genomes]
rs4852861	0.93[ASN][1000 genomes]
rs4852862	0.86[ASN][1000 genomes]
rs55877105	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62147579	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546750	0.81[ASN][1000 genomes]
rs6546752	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6546753	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs6546755	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6719255	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6748607	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6751276	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6760895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs7559131	0.87[GIH][hapmap]
rs7565922	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7583271	0.87[GIH][hapmap]
rs768042	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs768043	0.93[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9679148	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41401	MOGS	cis	cerebellum	SCAN
rs41401	TGFA	cis	cerebellum	SCAN
rs41401	PNO1	cis	parietal	SCAN
rs41401	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72406400-72425800	Weak transcription	Brain Anterior Caudate	brain
2	chr2:72406800-72419800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:72407200-72425200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:72407800-72424600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:72409600-72426000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:72410600-72420000	Weak transcription	A549	lung
7	chr2:72412800-72421600	Weak transcription	Gastric	stomach
8	chr2:72412800-72425400	Weak transcription	Stomach Mucosa	stomach
9	chr2:72412800-72429800	Weak transcription	Right Ventricle	heart
10	chr2:72412800-72431000	Weak transcription	Left Ventricle	heart
11	chr2:72415200-72426000	Weak transcription	NHEK	skin
12	chr2:72415400-72424400	Weak transcription	Aorta	Aorta
13	chr2:72415400-72426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:72415400-72430800	Weak transcription	Placenta	Placenta
15	chr2:72418600-72419400	Enhancers	Brain Angular Gyrus	brain
16	chr2:72418800-72419600	Enhancers	Brain Substantia Nigra	brain
17	chr2:72419000-72419800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:72419000-72420200	Weak transcription	Fetal Lung	lung
19	chr2:72419000-72430800	Weak transcription	Small Intestine	intestine

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