Variant report

Variant	rs11828904
Chromosome Location	chr11:73139116-73139117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1002127	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10501411	0.89[CEU][hapmap]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11235759	1.00[JPT][hapmap]
rs11235770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11235775	1.00[JPT][hapmap]
rs11235809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11544310	0.90[EUR][1000 genomes]
rs11820929	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11821094	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11823923	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11824614	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11826896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11826909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12275766	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12276892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12277924	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12282282	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12282790	1.00[JPT][hapmap]
rs12285885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12288753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12290623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12290701	0.83[ASN][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17132115	0.83[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap]
rs17244616	1.00[CEU][hapmap]
rs17310361	1.00[CEU][hapmap]
rs17310374	1.00[CEU][hapmap]
rs17851510	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1894076	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1938777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2027760	0.89[CEU][hapmap]
rs2027761	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2027763	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298807	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28641751	0.88[ASN][1000 genomes]
rs3741149	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3741152	0.89[CEU][hapmap]
rs3825005	1.00[JPT][hapmap]
rs3933402	1.00[JPT][hapmap]
rs57354084	0.84[EUR][1000 genomes]
rs58334887	0.82[EUR][1000 genomes]
rs60860405	0.83[ASN][1000 genomes]
rs61516411	0.86[AMR][1000 genomes]
rs6592521	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7102197	1.00[JPT][hapmap]
rs7105681	0.89[CEU][hapmap]
rs7110369	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7112924	0.90[EUR][1000 genomes]
rs7113420	1.00[JPT][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7115055	1.00[CEU][hapmap]
rs7115806	0.89[CEU][hapmap]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7122825	0.89[CEU][hapmap]
rs7123298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7123985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7125598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7125949	0.89[CEU][hapmap]
rs7125978	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7129990	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7131383	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap]
rs725103	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7342205	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs73543000	0.83[EUR][1000 genomes]
rs73544710	0.84[EUR][1000 genomes]
rs73544711	0.82[EUR][1000 genomes]
rs73544716	0.82[EUR][1000 genomes]
rs73544720	0.82[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap]
rs7927344	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7930454	0.89[CEU][hapmap]
rs7930880	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7934218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7935948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7937066	0.83[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs7941359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7944099	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7944346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7945825	1.00[CEU][hapmap]
rs7951072	1.00[CEU][hapmap]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs876480	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs947837	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9888218	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11828904	FAM168A	cis	Whole Blood	GTEx
rs11828904	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:73115200-73149400	Weak transcription	Fetal Kidney	kidney
4	chr11:73120800-73140600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:73120800-73141200	Weak transcription	Esophagus	oesophagus
6	chr11:73120800-73149000	Weak transcription	Fetal Lung	lung
7	chr11:73120800-73149800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:73120800-73150000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:73121000-73150200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:73122400-73163200	Weak transcription	Aorta	Aorta
11	chr11:73122800-73149600	Weak transcription	Gastric	stomach
12	chr11:73123800-73209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:73124000-73140800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:73126600-73149400	Weak transcription	Small Intestine	intestine
15	chr11:73128600-73139400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:73128600-73139400	Weak transcription	NHDF-Ad	bronchial
17	chr11:73129400-73152400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:73129600-73140000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:73129600-73147000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:73129600-73149400	Weak transcription	Liver	Liver
21	chr11:73129600-73150000	Weak transcription	Fetal Intestine Small	intestine
22	chr11:73129800-73141200	Weak transcription	Fetal Brain Male	brain
23	chr11:73130400-73141200	Weak transcription	Pancreas	Pancrea
24	chr11:73130600-73139200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:73130600-73139400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:73130600-73141000	Weak transcription	Thymus	Thymus
27	chr11:73130800-73140000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:73130800-73140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:73130800-73150000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:73131000-73140400	Weak transcription	Fetal Intestine Large	intestine
31	chr11:73131000-73190000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:73131200-73142800	Weak transcription	Brain Germinal Matrix	brain
33	chr11:73131200-73143200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:73131200-73149800	Weak transcription	Fetal Brain Female	brain
35	chr11:73131400-73141200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:73131600-73140000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:73131600-73145600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:73131800-73140000	Weak transcription	Dnd41	blood
39	chr11:73131800-73140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:73131800-73141000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr11:73132000-73143400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:73132000-73145200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr11:73132000-73150200	Weak transcription	HepG2	liver
44	chr11:73132600-73162600	Weak transcription	Primary B cells from cord blood	blood
45	chr11:73132800-73139800	Weak transcription	Primary T cells from cord blood	blood
46	chr11:73133000-73140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:73133000-73141000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr11:73133000-73146000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:73133200-73140600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:73133200-73145600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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