Variant report

Variant	rs10898458
Chromosome Location	chr11:85968037-85968038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85967045..85968879-chr11:85987127..85988641,2	K562	blood:
2	chr11:85967614..85970637-chr11:85971235..85974775,4	K562	blood:
3	chr11:85966228..85969859-chr11:85975228..85979391,4	K562	blood:

Variant related genes	Relation type
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10751137	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792841	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792843	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898448	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898449	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898452	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10898457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898459	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10898461	0.93[EUR][1000 genomes]
rs10898462	0.91[EUR][1000 genomes]
rs10898463	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs11234594	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234596	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12284085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466804	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1497725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874694	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270680	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270681	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3758881	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6592279	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7101712	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120070	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7924472	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7942971	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7950820	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991435	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10898458	C11orf73	Cis_1M	lymphoblastoid	RTeQTL
rs10898458	EED	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957200-85972400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:85957200-85972400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:85957200-85972400	Weak transcription	Esophagus	oesophagus
4	chr11:85957200-85995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:85957400-85985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
7	chr11:85957800-85968600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:85957800-85968600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:85957800-85997200	Weak transcription	Colonic Mucosa	Colon
10	chr11:85957800-85999800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:85958400-85972400	Weak transcription	Aorta	Aorta
12	chr11:85958400-85997200	Weak transcription	Brain Germinal Matrix	brain
13	chr11:85959200-85974000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:85959200-85988000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:85959200-85988600	Weak transcription	Brain Angular Gyrus	brain
16	chr11:85959200-85997600	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:85959400-85995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:85960000-85970800	Weak transcription	Fetal Brain Female	brain
19	chr11:85960000-85972400	Weak transcription	Pancreas	Pancrea
20	chr11:85960200-85972800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:85960200-85985600	Weak transcription	Gastric	stomach
22	chr11:85960600-85972200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:85960800-85972400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:85960800-85988000	Weak transcription	Fetal Heart	heart
25	chr11:85961000-85972200	Weak transcription	Ovary	ovary
26	chr11:85961000-85972400	Weak transcription	Right Ventricle	heart
27	chr11:85961000-85996000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:85961000-85997000	Weak transcription	Stomach Mucosa	stomach
29	chr11:85961200-85972600	Weak transcription	NHEK	skin
30	chr11:85961400-85980600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:85961400-85985800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:85961600-85968600	Weak transcription	Fetal Lung	lung
33	chr11:85961600-85970600	Weak transcription	A549	lung
34	chr11:85961600-85972400	Weak transcription	Small Intestine	intestine
35	chr11:85961600-85974400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:85961600-85998000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:85961800-85972400	Weak transcription	NHLF	lung
38	chr11:85961800-85988000	Weak transcription	Brain Substantia Nigra	brain
39	chr11:85962600-85968600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:85962600-85968600	Weak transcription	Osteobl	bone
41	chr11:85962800-85968600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:85962800-85969600	Strong transcription	Hela-S3	cervix
43	chr11:85962800-85972400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:85962800-85975200	Weak transcription	NHDF-Ad	bronchial
45	chr11:85963000-85968400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:85963000-85968400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:85963000-85984400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr11:85963800-85970800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:85964000-85968600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:85964000-85972400	Weak transcription	Lung	lung

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