Variant report

Variant	rs1207438
Chromosome Location	chr2:206185567-206185568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 197 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:196)

rs_ID	r²[population]
rs10199654	0.83[ASN][1000 genomes]
rs10490290	0.86[ASN][1000 genomes]
rs10490292	0.85[ASN][1000 genomes]
rs10490293	0.86[ASN][1000 genomes]
rs10490295	0.85[ASN][1000 genomes]
rs10804147	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10804148	0.82[ASN][1000 genomes]
rs10932102	0.84[ASN][1000 genomes]
rs10932104	0.88[ASN][1000 genomes]
rs10932105	0.88[ASN][1000 genomes]
rs10932106	0.88[ASN][1000 genomes]
rs10932107	0.86[ASN][1000 genomes]
rs10932108	0.86[ASN][1000 genomes]
rs10932109	0.85[ASN][1000 genomes]
rs1113314	0.83[ASN][1000 genomes]
rs11676344	0.85[ASN][1000 genomes]
rs11676518	0.86[ASN][1000 genomes]
rs11676519	0.86[ASN][1000 genomes]
rs11676529	0.86[ASN][1000 genomes]
rs11677457	0.88[ASN][1000 genomes]
rs11686270	0.86[ASN][1000 genomes]
rs11690439	0.81[ASN][1000 genomes]
rs11690480	0.88[ASN][1000 genomes]
rs11690561	0.88[ASN][1000 genomes]
rs11691342	0.85[ASN][1000 genomes]
rs11691345	0.90[ASN][1000 genomes]
rs11692923	0.84[ASN][1000 genomes]
rs11695465	0.88[ASN][1000 genomes]
rs1207411	0.92[ASN][1000 genomes]
rs1207415	0.93[ASN][1000 genomes]
rs1207420	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1207421	0.91[ASN][1000 genomes]
rs1207424	0.88[ASN][1000 genomes]
rs1207426	0.93[ASN][1000 genomes]
rs1207428	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1207429	0.91[ASN][1000 genomes]
rs1207430	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1207431	0.93[ASN][1000 genomes]
rs1207432	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1207433	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1207434	0.98[ASN][1000 genomes]
rs1207435	1.00[ASN][1000 genomes]
rs1207436	1.00[ASN][1000 genomes]
rs1207437	1.00[ASN][1000 genomes]
rs1207440	0.93[ASN][1000 genomes]
rs1207441	0.93[ASN][1000 genomes]
rs1211319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1212609	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12373584	0.86[ASN][1000 genomes]
rs12373610	0.86[ASN][1000 genomes]
rs12464688	0.86[ASN][1000 genomes]
rs12464755	0.84[ASN][1000 genomes]
rs12468755	0.90[ASN][1000 genomes]
rs12468794	0.90[ASN][1000 genomes]
rs12468975	0.86[ASN][1000 genomes]
rs12470003	0.86[ASN][1000 genomes]
rs12470079	0.86[ASN][1000 genomes]
rs12470434	0.90[ASN][1000 genomes]
rs12472752	0.83[ASN][1000 genomes]
rs12472815	0.83[ASN][1000 genomes]
rs12476682	0.88[ASN][1000 genomes]
rs12615597	0.84[ASN][1000 genomes]
rs12622101	0.84[ASN][1000 genomes]
rs12623757	0.88[ASN][1000 genomes]
rs12989507	0.88[ASN][1000 genomes]
rs12995657	0.85[ASN][1000 genomes]
rs13000324	0.86[ASN][1000 genomes]
rs13004164	0.90[ASN][1000 genomes]
rs13004568	0.83[ASN][1000 genomes]
rs13009974	0.88[ASN][1000 genomes]
rs13011880	0.88[ASN][1000 genomes]
rs13011981	0.88[ASN][1000 genomes]
rs13015412	0.92[ASN][1000 genomes]
rs13017922	0.82[ASN][1000 genomes]
rs13021602	0.85[ASN][1000 genomes]
rs13022810	0.82[ASN][1000 genomes]
rs13024741	0.82[ASN][1000 genomes]
rs13024952	1.00[ASN][1000 genomes]
rs13025642	0.80[ASN][1000 genomes]
rs13028215	0.83[ASN][1000 genomes]
rs13033820	0.83[ASN][1000 genomes]
rs1398053	0.86[ASN][1000 genomes]
rs1398054	0.86[ASN][1000 genomes]
rs1511873	0.88[ASN][1000 genomes]
rs1511874	0.88[ASN][1000 genomes]
rs1540365	0.84[ASN][1000 genomes]
rs1540366	0.84[ASN][1000 genomes]
rs1540367	0.83[ASN][1000 genomes]
rs1540368	0.83[ASN][1000 genomes]
rs1606237	0.85[ASN][1000 genomes]
rs1606238	0.88[ASN][1000 genomes]
rs1606239	0.88[ASN][1000 genomes]
rs17201041	0.88[ASN][1000 genomes]
rs1849226	0.80[ASN][1000 genomes]
rs1861508	0.84[ASN][1000 genomes]
rs1861509	0.84[ASN][1000 genomes]
rs1861510	0.94[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1861511	0.85[ASN][1000 genomes]
rs1861513	0.93[ASN][1000 genomes]
rs1861514	0.88[ASN][1000 genomes]
rs1877338	0.86[ASN][1000 genomes]
rs1877339	0.86[ASN][1000 genomes]
rs1912845	0.80[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1921805	0.84[ASN][1000 genomes]
rs1990667	0.89[ASN][1000 genomes]
rs2041877	0.88[ASN][1000 genomes]
rs2080418	0.80[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2080419	0.88[ASN][1000 genomes]
rs2137176	0.86[ASN][1000 genomes]
rs2160453	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2160455	0.90[ASN][1000 genomes]
rs2193077	0.91[ASN][1000 genomes]
rs2216176	0.86[ASN][1000 genomes]
rs2247282	0.84[ASN][1000 genomes]
rs2251539	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2336416	0.84[ASN][1000 genomes]
rs2336420	0.86[ASN][1000 genomes]
rs2541148	0.83[ASN][1000 genomes]
rs2541149	0.90[ASN][1000 genomes]
rs2541150	0.93[ASN][1000 genomes]
rs2541151	1.00[ASN][1000 genomes]
rs2541152	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2541153	1.00[ASN][1000 genomes]
rs2541154	1.00[ASN][1000 genomes]
rs2541160	0.93[ASN][1000 genomes]
rs2668144	0.93[ASN][1000 genomes]
rs2668145	0.93[ASN][1000 genomes]
rs2668146	0.93[ASN][1000 genomes]
rs2668148	0.94[ASN][1000 genomes]
rs2704638	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704643	0.93[ASN][1000 genomes]
rs2704644	1.00[ASN][1000 genomes]
rs2878692	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34226321	0.83[ASN][1000 genomes]
rs34332011	0.85[ASN][1000 genomes]
rs34486316	0.86[ASN][1000 genomes]
rs35337631	0.86[ASN][1000 genomes]
rs35550118	0.92[ASN][1000 genomes]
rs35655292	0.85[ASN][1000 genomes]
rs3843339	0.90[ASN][1000 genomes]
rs3845806	0.90[ASN][1000 genomes]
rs3856509	0.84[ASN][1000 genomes]
rs3928642	0.90[ASN][1000 genomes]
rs4119079	0.84[ASN][1000 genomes]
rs4119081	0.84[ASN][1000 genomes]
rs4505506	0.84[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4595957	0.85[ASN][1000 genomes]
rs4673317	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4673318	0.84[ASN][1000 genomes]
rs4673319	0.90[ASN][1000 genomes]
rs4673320	0.88[ASN][1000 genomes]
rs4673323	0.88[ASN][1000 genomes]
rs4673324	0.88[ASN][1000 genomes]
rs4673325	0.85[ASN][1000 genomes]
rs4673326	0.86[ASN][1000 genomes]
rs4673327	0.86[ASN][1000 genomes]
rs4673328	0.86[ASN][1000 genomes]
rs4673329	0.85[ASN][1000 genomes]
rs4673330	0.85[ASN][1000 genomes]
rs4675508	0.82[ASN][1000 genomes]
rs4675511	0.84[ASN][1000 genomes]
rs4675512	0.98[ASN][1000 genomes]
rs4675513	0.84[ASN][1000 genomes]
rs4675515	0.90[ASN][1000 genomes]
rs4675519	0.88[ASN][1000 genomes]
rs4675521	0.83[ASN][1000 genomes]
rs55850246	0.84[ASN][1000 genomes]
rs62171496	1.00[ASN][1000 genomes]
rs62171506	0.88[ASN][1000 genomes]
rs66583439	0.86[ASN][1000 genomes]
rs6740963	0.86[ASN][1000 genomes]
rs6755865	0.85[ASN][1000 genomes]
rs6756234	0.83[ASN][1000 genomes]
rs6761373	0.90[ASN][1000 genomes]
rs7582340	0.86[ASN][1000 genomes]
rs7594732	0.84[ASN][1000 genomes]
rs849189	1.00[ASN][1000 genomes]
rs849193	0.98[ASN][1000 genomes]
rs849194	1.00[ASN][1000 genomes]
rs849198	0.93[ASN][1000 genomes]
rs849200	0.93[ASN][1000 genomes]
rs849207	0.93[ASN][1000 genomes]
rs849208	0.91[ASN][1000 genomes]
rs849216	0.98[ASN][1000 genomes]
rs849218	1.00[ASN][1000 genomes]
rs849219	1.00[ASN][1000 genomes]
rs849220	0.99[ASN][1000 genomes]
rs849221	1.00[ASN][1000 genomes]
rs849222	1.00[ASN][1000 genomes]
rs849223	1.00[ASN][1000 genomes]
rs849224	0.94[ASN][1000 genomes]
rs849250	0.97[ASN][1000 genomes]
rs907462	0.92[ASN][1000 genomes]
rs964896	0.86[ASN][1000 genomes]
rs964897	0.86[ASN][1000 genomes]
rs979187	0.88[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	nsv1012780	chr2:206124954-206546271	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1207438	FAM119A	cis	cerebellum	SCAN
rs1207438	NDUFB3	cis	parietal	SCAN
rs1207438	CASP8	cis	cerebellum	SCAN
rs1207438	ALS2CR12	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:206168600-206190600	Weak transcription	Fetal Intestine Large	intestine
2	chr2:206171000-206186200	Weak transcription	HSMMtube	muscle
3	chr2:206171000-206190200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:206178600-206186200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:206180800-206188200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:206182400-206187000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:206184000-206185600	Weak transcription	Left Ventricle	heart
8	chr2:206185000-206187000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:206185200-206187000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:206185400-206186800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:206185400-206186800	Enhancers	HSMM	muscle

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