Variant report

Variant	rs2729753
Chromosome Location	chr11:77077274-77077275
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10899376	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs10899378	0.81[EUR][1000 genomes]
rs10899379	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237173	0.83[EUR][1000 genomes]
rs11237189	0.80[EUR][1000 genomes]
rs11237193	0.81[EUR][1000 genomes]
rs11237195	0.81[CEU][hapmap]
rs1377470	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1377471	0.85[EUR][1000 genomes]
rs1670459	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1793476	0.86[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs1793483	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1840151	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250639	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2250647	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2298793	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2602458	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602459	0.82[EUR][1000 genomes]
rs2602463	0.97[ASN][1000 genomes]
rs2602464	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2602465	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602468	0.85[EUR][1000 genomes]
rs2602469	0.85[EUR][1000 genomes]
rs2602470	0.85[EUR][1000 genomes]
rs2602472	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602477	0.82[EUR][1000 genomes]
rs2602479	0.82[EUR][1000 genomes]
rs2602488	0.90[CEU][hapmap]
rs2602489	0.81[EUR][1000 genomes]
rs2725810	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2725812	0.91[JPT][hapmap]
rs2725815	0.81[EUR][1000 genomes]
rs2725816	0.83[EUR][1000 genomes]
rs2725826	0.81[EUR][1000 genomes]
rs2725827	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2725830	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2725831	0.85[EUR][1000 genomes]
rs2725832	0.84[EUR][1000 genomes]
rs2729747	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729762	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729769	0.81[EUR][1000 genomes]
rs2729771	0.97[ASN][1000 genomes]
rs2844328	0.82[EUR][1000 genomes]
rs2844332	0.82[EUR][1000 genomes]
rs2844333	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844334	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2844336	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844337	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2852384	0.82[EUR][1000 genomes]
rs2852385	0.84[EUR][1000 genomes]
rs2852392	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2852394	0.82[EUR][1000 genomes]
rs2853086	0.82[EUR][1000 genomes]
rs2853087	0.82[EUR][1000 genomes]
rs2853088	0.80[EUR][1000 genomes]
rs2853090	0.82[EUR][1000 genomes]
rs2853103	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs3015989	0.86[JPT][hapmap]
rs3015993	0.86[JPT][hapmap]
rs476925	0.95[JPT][hapmap]
rs478134	0.82[ASN][1000 genomes]
rs489038	0.80[ASN][1000 genomes]
rs4945162	0.91[JPT][hapmap]
rs4945166	0.91[JPT][hapmap]
rs495889	0.86[JPT][hapmap]
rs497172	0.83[ASN][1000 genomes]
rs497946	0.83[ASN][1000 genomes]
rs514191	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs539906	0.84[ASN][1000 genomes]
rs561153	0.84[ASN][1000 genomes]
rs562939	0.84[ASN][1000 genomes]
rs575662	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs576079	0.83[ASN][1000 genomes]
rs584909	0.84[ASN][1000 genomes]
rs599437	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs605910	0.84[ASN][1000 genomes]
rs614775	0.82[ASN][1000 genomes]
rs618012	0.84[ASN][1000 genomes]
rs667331	0.83[ASN][1000 genomes]
rs674652	0.86[JPT][hapmap]
rs688212	0.95[JPT][hapmap]
rs7118869	0.95[JPT][hapmap]
rs7119033	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2729753	RELT	cis	cerebellum	SCAN
rs2729753	MRPL48	cis	cerebellum	SCAN
rs2729753	PAK1	cis	parietal	SCAN
rs2729753	UCP2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr11:77034400-77086200	Weak transcription	NHLF	lung
4	chr11:77042800-77080800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:77043400-77082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:77043400-77083600	Weak transcription	Thymus	Thymus
7	chr11:77043800-77088400	Weak transcription	Colonic Mucosa	Colon
8	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:77047400-77089000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:77048600-77087800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:77052600-77085600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:77055000-77085000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr11:77055200-77083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
18	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
19	chr11:77057400-77088000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:77059800-77085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:77059800-77088800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:77060400-77084000	Weak transcription	Fetal Stomach	stomach
23	chr11:77063200-77081000	Weak transcription	Stomach Mucosa	stomach
24	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
25	chr11:77064600-77083000	Weak transcription	Brain Anterior Caudate	brain
26	chr11:77064600-77085400	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:77064800-77085200	Weak transcription	Osteobl	bone
28	chr11:77066000-77084000	Weak transcription	Colon Smooth Muscle	Colon
29	chr11:77066800-77090000	Weak transcription	Brain Angular Gyrus	brain
30	chr11:77067000-77085600	Weak transcription	A549	lung
31	chr11:77067000-77088000	Weak transcription	Gastric	stomach
32	chr11:77067000-77088200	Weak transcription	Liver	Liver
33	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
35	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
36	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:77067600-77083000	Weak transcription	Fetal Kidney	kidney
38	chr11:77068400-77083400	Weak transcription	Aorta	Aorta
39	chr11:77068600-77085600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:77068600-77085800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:77068800-77097000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:77069000-77083400	Weak transcription	HMEC	breast
43	chr11:77069000-77090000	Weak transcription	Fetal Lung	lung
44	chr11:77069200-77086000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:77069600-77085400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:77070000-77078200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:77070000-77083200	Weak transcription	Brain Germinal Matrix	brain
48	chr11:77070000-77083800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:77070200-77081200	Weak transcription	Rectal Mucosa Donor 31	rectum

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