Variant report

Variant	rs2602472
Chromosome Location	chr11:77068154-77068155
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1037452	0.83[AFR][1000 genomes]
rs10899365	0.80[TSI][hapmap]
rs10899376	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs10899377	0.83[AFR][1000 genomes]
rs10899378	0.93[EUR][1000 genomes]
rs10899379	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11237173	0.97[EUR][1000 genomes]
rs11237189	0.92[EUR][1000 genomes]
rs11237190	0.85[AFR][1000 genomes]
rs11237193	0.93[EUR][1000 genomes]
rs11237195	0.90[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11237196	0.91[EUR][1000 genomes]
rs11237199	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs11820118	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs11828786	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12223138	0.85[AFR][1000 genomes]
rs12271542	0.91[EUR][1000 genomes]
rs1377470	0.95[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1377471	0.98[EUR][1000 genomes]
rs1453341	0.83[AFR][1000 genomes]
rs1453343	0.92[EUR][1000 genomes]
rs1618188	0.80[TSI][hapmap]
rs1670459	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs17135670	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs1793476	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs1793483	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1793488	0.80[TSI][hapmap]
rs1840151	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250639	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs2250647	0.95[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs2298793	0.95[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2467481	0.86[AFR][1000 genomes]
rs2602458	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602459	0.94[EUR][1000 genomes]
rs2602461	0.85[AFR][1000 genomes]
rs2602463	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602464	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2602465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602468	0.98[EUR][1000 genomes]
rs2602469	0.98[EUR][1000 genomes]
rs2602470	0.98[EUR][1000 genomes]
rs2602471	0.93[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2602474	0.93[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2602475	0.83[YRI][hapmap]
rs2602477	0.94[EUR][1000 genomes]
rs2602479	0.94[EUR][1000 genomes]
rs2602488	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs2602489	0.91[EUR][1000 genomes]
rs2725810	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2725812	0.82[JPT][hapmap]
rs2725815	0.91[EUR][1000 genomes]
rs2725816	0.96[EUR][1000 genomes]
rs2725826	0.92[EUR][1000 genomes]
rs2725827	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2725830	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2725831	0.98[EUR][1000 genomes]
rs2725832	0.97[EUR][1000 genomes]
rs2729747	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729749	0.87[AFR][1000 genomes]
rs2729752	0.87[AFR][1000 genomes]
rs2729753	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729756	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs2729762	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729763	0.84[AFR][1000 genomes]
rs2729769	0.91[EUR][1000 genomes]
rs2729771	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844327	0.93[LWK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2844328	0.94[EUR][1000 genomes]
rs2844332	0.94[EUR][1000 genomes]
rs2844333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844334	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2844336	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844337	0.95[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2852384	0.94[EUR][1000 genomes]
rs2852385	0.97[EUR][1000 genomes]
rs2852392	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2852394	0.94[EUR][1000 genomes]
rs2853085	0.93[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2853086	0.94[EUR][1000 genomes]
rs2853087	0.94[EUR][1000 genomes]
rs2853088	0.92[EUR][1000 genomes]
rs2853090	0.95[EUR][1000 genomes]
rs2853095	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2853097	0.80[ASN][1000 genomes]
rs2853098	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs2853103	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs2888377	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs3015989	0.95[JPT][hapmap]
rs3015993	0.95[JPT][hapmap]
rs4590893	0.90[EUR][1000 genomes]
rs476925	0.87[JPT][hapmap]
rs492527	0.83[ASN][1000 genomes]
rs4944159	0.84[AFR][1000 genomes]
rs4944160	0.83[AFR][1000 genomes]
rs4945162	0.83[JPT][hapmap]
rs4945166	0.83[JPT][hapmap]
rs495889	0.95[JPT][hapmap]
rs514191	0.87[JPT][hapmap]
rs556696	0.83[ASN][1000 genomes]
rs568309	0.81[ASN][1000 genomes]
rs575662	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs599437	0.87[JPT][hapmap]
rs639857	0.84[ASN][1000 genomes]
rs674652	0.95[JPT][hapmap]
rs688212	0.87[JPT][hapmap]
rs7105662	0.85[AFR][1000 genomes]
rs7109645	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7118869	0.87[JPT][hapmap]
rs7119033	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs724369	0.86[AFR][1000 genomes]
rs7943778	0.81[EUR][1000 genomes]
rs876319	0.93[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2602472	RELT	cis	cerebellum	SCAN
rs2602472	UCP2	cis	cerebellum	SCAN
rs2602472	PAK1	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77028000-77068400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:77031600-77073800	Weak transcription	Spleen	Spleen
4	chr11:77031800-77070400	Weak transcription	Fetal Brain Male	brain
5	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:77034400-77086200	Weak transcription	NHLF	lung
7	chr11:77042800-77080800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:77043400-77072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:77043400-77074800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:77043400-77082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:77043400-77083600	Weak transcription	Thymus	Thymus
12	chr11:77043800-77071400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:77043800-77088400	Weak transcription	Colonic Mucosa	Colon
14	chr11:77044200-77075000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:77044600-77071600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:77046200-77077000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:77047400-77089000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:77047800-77075000	Weak transcription	Left Ventricle	heart
23	chr11:77047800-77075600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:77048600-77069200	Weak transcription	Brain Germinal Matrix	brain
25	chr11:77048600-77070000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:77048600-77087800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:77048800-77069000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr11:77050400-77072000	Strong transcription	Primary T cells from cord blood	blood
29	chr11:77052600-77085600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:77054000-77068200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:77055000-77085000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr11:77055200-77083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
34	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
35	chr11:77057400-77088000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:77057600-77069200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr11:77058600-77068200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:77058600-77075000	Weak transcription	NH-A	brain
39	chr11:77059600-77069600	Weak transcription	Ovary	ovary
40	chr11:77059800-77085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:77059800-77088800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr11:77060000-77068200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:77060400-77084000	Weak transcription	Fetal Stomach	stomach
44	chr11:77061000-77069200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:77063000-77070400	Strong transcription	Primary B cells from cord blood	blood
46	chr11:77063000-77072000	Weak transcription	NHDF-Ad	bronchial
47	chr11:77063200-77081000	Weak transcription	Stomach Mucosa	stomach
48	chr11:77063400-77070200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:77063400-77070400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:77063400-77070400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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