Variant report

Variant	rs10898459
Chromosome Location	chr11:85972939-85972940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:85972282-85973052	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:85972830-85973014	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:85972032-85973101	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:85972185-85973071	GM12892	blood:	n/a	n/a
5	POLR2A	chr11:85972341-85973007	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:85972209-85972957	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:85972180-85973080	K562	blood:	n/a	n/a
8	POLR2A	chr11:85972351-85973489	K562	blood:	n/a	n/a
9	POLR2A	chr11:85972201-85973051	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:85972155-85973044	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:85972238-85973026	GM12891	blood:	n/a	n/a
12	POLR2A	chr11:85972370-85972971	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85971654..85973609-chr11:85974451..85977409,3	K562	blood:
2	chr11:85954989..85958031-chr11:85971224..85974076,3	MCF-7	breast:
3	chr11:85970225..85973154-chr11:85973663..85975951,2	K562	blood:
4	chr11:85967614..85970637-chr11:85971235..85974775,4	K562	blood:
5	chr11:85961896..85964300-chr11:85972097..85973858,2	K562	blood:
6	chr11:85971469..85973576-chr11:86002289..86004505,2	MCF-7	breast:

No data

Variant related genes	Relation type
EED	TF binding region
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10751137	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs10792841	0.94[EUR][1000 genomes]
rs10792842	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10792843	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10898449	0.81[EUR][1000 genomes]
rs10898452	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898457	0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10898458	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10898461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234594	0.94[EUR][1000 genomes]
rs11234596	0.82[EUR][1000 genomes]
rs12284085	0.93[EUR][1000 genomes]
rs1466804	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1497725	0.95[EUR][1000 genomes]
rs1497726	0.94[EUR][1000 genomes]
rs1874694	0.90[EUR][1000 genomes]
rs2270680	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2270681	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes]
rs3758881	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs6592279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs7101712	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7120070	0.87[EUR][1000 genomes]
rs7120222	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7924472	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7942971	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7950820	0.94[EUR][1000 genomes]
rs7951030	0.96[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7951188	0.94[EUR][1000 genomes]
rs974144	0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs991435	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	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
2	nsv898055	chr11:85968623-86000757	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10898459	EED	Cis_1M	lymphoblastoid	RTeQTL
rs10898459	C11orf73	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957200-85995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:85957400-85985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
4	chr11:85957800-85997200	Weak transcription	Colonic Mucosa	Colon
5	chr11:85957800-85999800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:85958400-85997200	Weak transcription	Brain Germinal Matrix	brain
7	chr11:85959200-85974000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:85959200-85988000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:85959200-85988600	Weak transcription	Brain Angular Gyrus	brain
10	chr11:85959200-85997600	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:85959400-85995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:85960200-85985600	Weak transcription	Gastric	stomach
13	chr11:85960800-85988000	Weak transcription	Fetal Heart	heart
14	chr11:85961000-85996000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:85961000-85997000	Weak transcription	Stomach Mucosa	stomach
16	chr11:85961400-85980600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:85961400-85985800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:85961600-85974400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:85961600-85998000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:85961800-85988000	Weak transcription	Brain Substantia Nigra	brain
21	chr11:85962800-85975200	Weak transcription	NHDF-Ad	bronchial
22	chr11:85963000-85984400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:85964000-85995000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:85964400-85980000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:85964400-85987600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:85965800-85975400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:85965800-85976400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:85966000-85992000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:85966200-85976200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:85966200-85991600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr11:85966400-85975600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:85966400-85976400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:85966400-85976600	Strong transcription	Fetal Thymus	thymus
34	chr11:85966400-85978600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:85967000-85973200	Strong transcription	HSMM	muscle
36	chr11:85967000-85991600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:85967200-85977600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:85967400-85975800	Strong transcription	Primary T cells from cord blood	blood
39	chr11:85967600-85975000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr11:85967800-85974800	Strong transcription	Thymus	Thymus
41	chr11:85967800-85975400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:85967800-85978600	Strong transcription	Placenta	Placenta
43	chr11:85967800-85981200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:85968000-85974000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:85968000-85975000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:85968200-85974600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:85968800-85988800	Weak transcription	HSMMtube	muscle
48	chr11:85969000-85973800	Weak transcription	HepG2	liver
49	chr11:85969000-85974000	Weak transcription	Brain Anterior Caudate	brain
50	chr11:85969200-85973800	Weak transcription	H1 Cell Line	embryonic stem cell

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