Variant report

Variant	rs194235
Chromosome Location	chr2:72430862-72430863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:113)

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]
rs10182075	1.00[YRI][hapmap]
rs10186006	1.00[YRI][hapmap]
rs10190799	1.00[ASN][1000 genomes]
rs10192800	0.92[CEU][hapmap];0.85[EUR][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];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs10209861	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];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];0.85[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];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs11681809	0.86[ASN][1000 genomes]
rs12151496	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12466026	1.00[CHB][hapmap]
rs12466112	1.00[CHB][hapmap]
rs13389524	1.00[CHB][hapmap]
rs13391463	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13395204	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13425458	1.00[YRI][hapmap]
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]
rs194236	0.81[ASN][1000 genomes]
rs194237	0.86[ASN][1000 genomes]
rs194238	0.86[ASN][1000 genomes]
rs194239	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	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041564	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2080044	1.00[CHB][hapmap]
rs2109963	1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2159823	1.00[CHB][hapmap]
rs2192014	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
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	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[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	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[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]
rs41401	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]
rs41402	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.84[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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41406	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[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	0.87[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41411	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41412	0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41413	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]
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	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4852288	0.87[GIH][hapmap]
rs4852860	0.86[ASN][1000 genomes]
rs4852861	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4852862	0.86[ASN][1000 genomes]
rs55877105	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62147579	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546750	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546752	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6546753	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546755	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6719255	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6748607	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6751276	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6760895	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7559131	0.87[GIH][hapmap]
rs7565922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7583271	0.87[GIH][hapmap]
rs768042	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs768043	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9679148	0.83[EUR][1000 genomes];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs194235	MOGS	cis	cerebellum	SCAN
rs194235	TPRKB	cis	cerebellum	SCAN
rs194235	TGFA	cis	cerebellum	SCAN
rs194235	MPHOSPH10	cis	cerebellum	SCAN
rs194235	PCYOX1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72412800-72431000	Weak transcription	Left Ventricle	heart
2	chr2:72426200-72431000	Weak transcription	Gastric	stomach
3	chr2:72426200-72431400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:72426200-72431400	Weak transcription	NHLF	lung
5	chr2:72426600-72432000	Weak transcription	HSMM	muscle
6	chr2:72426800-72437600	Weak transcription	NH-A	brain
7	chr2:72427000-72431000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:72427000-72431800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:72427000-72432000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:72427000-72432000	Weak transcription	Osteobl	bone
11	chr2:72427000-72432200	Weak transcription	NHDF-Ad	bronchial
12	chr2:72428800-72431400	Enhancers	A549	lung
13	chr2:72429000-72433200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:72429200-72433600	Enhancers	Fetal Intestine Large	intestine
15	chr2:72429400-72433000	Enhancers	Fetal Lung	lung
16	chr2:72429800-72433200	Enhancers	Right Ventricle	heart
17	chr2:72430000-72431400	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:72430000-72433200	Enhancers	Ovary	ovary
19	chr2:72430200-72433400	Enhancers	Brain Substantia Nigra	brain
20	chr2:72430400-72433200	Enhancers	Colon Smooth Muscle	Colon
21	chr2:72430400-72433600	Enhancers	Fetal Stomach	stomach
22	chr2:72430600-72431400	Enhancers	HMEC	breast
23	chr2:72430600-72433400	Enhancers	Brain Anterior Caudate	brain
24	chr2:72430800-72431000	Enhancers	Fetal Heart	heart
25	chr2:72430800-72431200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:72430800-72431200	Weak transcription	Brain Angular Gyrus	brain
27	chr2:72430800-72431200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:72430800-72431400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:72430800-72431400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:72430800-72431400	Enhancers	Placenta	Placenta
31	chr2:72430800-72431400	Enhancers	HepG2	liver
32	chr2:72430800-72431400	Enhancers	NHEK	skin
33	chr2:72430800-72432800	Enhancers	Liver	Liver
34	chr2:72430800-72432800	Enhancers	Colonic Mucosa	Colon
35	chr2:72430800-72432800	Enhancers	Esophagus	oesophagus
36	chr2:72430800-72433000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:72430800-72433000	Enhancers	Pancreas	Pancrea
38	chr2:72430800-72433200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:72430800-72433200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:72430800-72433200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:72430800-72433200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:72430800-72433200	Enhancers	Fetal Kidney	kidney
43	chr2:72430800-72433200	Enhancers	Fetal Muscle Leg	muscle
44	chr2:72430800-72433200	Enhancers	Right Atrium	heart
45	chr2:72430800-72433200	Enhancers	Stomach Mucosa	stomach
46	chr2:72430800-72433400	Enhancers	Fetal Intestine Small	intestine
47	chr2:72430800-72433600	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:72430800-72433600	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links