Variant report

Variant	rs11209935
Chromosome Location	chr1:72650254-72650255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1026566	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1026567	1.00[JPT][hapmap]
rs10493493	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs10493494	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11209923	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11209928	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11209932	0.90[ASN][1000 genomes]
rs11209933	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11209938	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11583451	0.95[ASN][1000 genomes]
rs11587829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11587895	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs1194265	0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1194267	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1194269	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1194270	1.00[JPT][hapmap]
rs1194271	0.82[ASN][1000 genomes]
rs1194273	0.82[ASN][1000 genomes]
rs1194277	0.82[ASN][1000 genomes]
rs1194282	0.82[ASN][1000 genomes]
rs1194283	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1194284	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1194286	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12036585	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1205484	0.82[ASN][1000 genomes]
rs1209251	0.82[ASN][1000 genomes]
rs12117225	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12124902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12125336	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12126162	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12136617	0.94[ASN][1000 genomes]
rs12137663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12139652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12141242	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342863	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342874	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1385920	0.95[ASN][1000 genomes]
rs1385921	0.95[ASN][1000 genomes]
rs1486097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1486111	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1675356	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17524209	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17525406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17588282	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17589316	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858600	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2066416	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2126077	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2153929	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298151	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298152	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2422136	0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2630431	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2797540	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2797543	0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2821283	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs2821285	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2821288	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2821293	1.00[JPT][hapmap]
rs2821295	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2821296	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55777234	0.95[ASN][1000 genomes]
rs56062633	0.83[ASN][1000 genomes]
rs56248439	0.83[ASN][1000 genomes]
rs6656980	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659016	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6668604	0.90[ASN][1000 genomes]
rs6698979	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6699731	0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6699841	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7349073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7517387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7518919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7529364	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7549778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs985227	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1006076	chr1:72477436-72700903	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv534996	chr1:72477436-72700903	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv461906	chr1:72549836-72683226	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv461917	chr1:72549836-72683226	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv546480	chr1:72549836-72683226	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
9	nsv461928	chr1:72555489-72683226	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
10	nsv546481	chr1:72555489-72683226	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
11	nsv461939	chr1:72555489-72717743	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv546482	chr1:72555489-72717743	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv546483	chr1:72581966-72659880	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
14	nsv997768	chr1:72583375-72665268	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
15	nsv546484	chr1:72595125-72667196	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
16	nsv1013250	chr1:72603540-72762582	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv528210	chr1:72606418-72659880	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
18	nsv470715	chr1:72606418-72659880	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
19	nsv1010315	chr1:72615648-72653421	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
20	nsv830192	chr1:72616562-72806118	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	nsv998410	chr1:72618544-72651819	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
22	nsv999081	chr1:72618544-72653421	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
23	nsv1009412	chr1:72618756-72651449	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	diseases
24	nsv1013666	chr1:72618756-72653421	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
25	nsv1000451	chr1:72618756-72658214	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
26	nsv516389	chr1:72621463-72657058	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
27	nsv461951	chr1:72634912-72707226	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
28	nsv546485	chr1:72634912-72707226	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
29	nsv1014832	chr1:72642420-72823477	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
30	nsv534997	chr1:72642420-72823477	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11209935	NEGR1	cis	cerebellum	SCAN
rs11209935	ANKRD13C	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72644400-72668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:72648600-72652000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:72648800-72651200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:72648800-72651200	Enhancers	Colon Smooth Muscle	Colon
5	chr1:72649000-72651000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:72649200-72651200	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr1:72649200-72651200	Enhancers	Rectal Smooth Muscle	rectum
8	chr1:72649200-72651400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:72649600-72650600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:72649800-72650400	Enhancers	Fetal Kidney	kidney
11	chr1:72649800-72650400	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:72649800-72655000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:72650000-72650600	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:72650000-72651000	Weak transcription	Osteobl	bone
15	chr1:72650200-72650600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:72650200-72650800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:72650200-72651200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:72650200-72651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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