Variant report

Variant	rs10898931
Chromosome Location	chr11:73388363-73388364
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10793065	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs10793066	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898930	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898936	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11235861	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235862	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235883	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11235884	0.82[ASN][1000 genomes]
rs11602887	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12420357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12788229	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12788426	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1525749	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs1632159	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1670537	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1670557	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1670564	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1670565	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1723843	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1723848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1792156	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1792160	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1792165	0.86[CHB][hapmap]
rs1792174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1792193	0.86[CHB][hapmap]
rs1792198	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1976911	0.80[EUR][1000 genomes]
rs2008734	0.84[CEU][hapmap]
rs2140893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2367187	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2367188	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2886816	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817514	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs3862797	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs7104603	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7119055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7925514	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7938731	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs868667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9705336	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv983043	chr11:73386105-73389105	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
7	esv12423	chr11:73386773-73388778	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
8	nsv390	chr11:73388188-73432899	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10898931	WDR71	cis	multi-tissue	Pritchard
rs10898931	MRPL48	cis	multi-tissue	Pritchard
rs10898931	MRPL48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73372400-73395400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:73372600-73388400	Weak transcription	Dnd41	blood
3	chr11:73372600-73394800	Weak transcription	Brain Germinal Matrix	brain
4	chr11:73372800-73388400	Weak transcription	NHLF	lung
5	chr11:73372800-73390600	Weak transcription	HUVEC	blood vessel
6	chr11:73374200-73391800	Weak transcription	Hela-S3	cervix
7	chr11:73374400-73427200	Weak transcription	A549	lung
8	chr11:73374800-73388800	Weak transcription	GM12878-XiMat	blood
9	chr11:73375200-73388400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:73375200-73388400	Weak transcription	Fetal Lung	lung
11	chr11:73375200-73388800	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:73375200-73404400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:73375400-73388400	Weak transcription	Brain Angular Gyrus	brain
14	chr11:73375800-73388400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:73375800-73400000	Weak transcription	Lung	lung
16	chr11:73375800-73416200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:73376000-73388400	Weak transcription	HepG2	liver
18	chr11:73376200-73388400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:73376200-73390400	Weak transcription	Brain Anterior Caudate	brain
20	chr11:73376200-73395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:73376200-73398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:73376600-73399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:73376600-73400000	Weak transcription	Spleen	Spleen
24	chr11:73376800-73388800	Weak transcription	Fetal Kidney	kidney
25	chr11:73377000-73400000	Weak transcription	Psoas Muscle	Psoas
26	chr11:73377200-73388600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:73379400-73388600	Weak transcription	K562	blood
28	chr11:73381400-73389000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:73381800-73400000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:73382200-73399000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr11:73382200-73436000	Weak transcription	Small Intestine	intestine
32	chr11:73382200-73441200	Weak transcription	Stomach Mucosa	stomach
33	chr11:73382400-73388800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:73382400-73421600	Weak transcription	Gastric	stomach
35	chr11:73382600-73388400	Weak transcription	Fetal Brain Female	brain
36	chr11:73382800-73388800	Weak transcription	Fetal Stomach	stomach
37	chr11:73382800-73400400	Weak transcription	Pancreas	Pancrea
38	chr11:73383200-73388400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:73383200-73388600	Weak transcription	Right Ventricle	heart
40	chr11:73383200-73399000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:73383400-73427200	Weak transcription	Fetal Heart	heart
42	chr11:73383800-73395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:73384000-73427600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:73384800-73401800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:73385200-73389800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:73385200-73391000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:73385200-73391200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:73385200-73392000	Strong transcription	Placenta	Placenta
50	chr11:73385200-73393600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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