Variant report

Variant	rs2270680
Chromosome Location	chr11:85961166-85961167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85961055..85963949-chr11:85977588..85979820,2	MCF-7	breast:
2	chr11:85961099..85962736-chr11:85974379..85975917,2	K562	blood:
3	chr11:85954444..85957790-chr11:85960392..85964072,7	MCF-7	breast:
4	chr11:85960754..85963363-chr12:2217354..2219874,2	MCF-7	breast:
5	chr11:85374101..85375834-chr11:85958556..85961533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074266	Chromatin interaction
ENSG00000137504	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	0.93[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792841	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792842	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792843	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898448	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898449	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898452	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10898457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898458	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]
rs10898459	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10898461	0.94[EUR][1000 genomes]
rs10898462	0.92[EUR][1000 genomes]
rs10898463	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11234594	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234596	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12284085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466804	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1497725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874694	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270681	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3758881	0.93[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6592279	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7101712	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120070	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7924472	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7942971	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs7950820	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951030	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]
rs7951188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991435	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.97[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
rs2270680	EED	Cis_1M	lymphoblastoid	RTeQTL
rs2270680	C11orf73	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957000-85963800	Weak transcription	Spleen	Spleen
2	chr11:85957200-85963800	Weak transcription	Lung	lung
3	chr11:85957200-85972400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:85957200-85972400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:85957200-85972400	Weak transcription	Esophagus	oesophagus
6	chr11:85957200-85995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:85957400-85961400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr11:85957400-85961600	Enhancers	Primary B cells from peripheral blood	blood
9	chr11:85957400-85962400	Weak transcription	Placenta	Placenta
10	chr11:85957400-85967600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:85957400-85985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
13	chr11:85957600-85961200	Enhancers	Primary T cells from cord blood	blood
14	chr11:85957600-85961600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr11:85957800-85961600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:85957800-85962000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr11:85957800-85962600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr11:85957800-85962800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:85957800-85967800	Weak transcription	Thymus	Thymus
20	chr11:85957800-85968000	Weak transcription	HSMMtube	muscle
21	chr11:85957800-85968600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:85957800-85968600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:85957800-85997200	Weak transcription	Colonic Mucosa	Colon
24	chr11:85957800-85999800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:85958000-85961600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr11:85958000-85963400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:85958200-85962400	Weak transcription	Osteobl	bone
28	chr11:85958400-85961200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr11:85958400-85961600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr11:85958400-85962200	Weak transcription	Fetal Thymus	thymus
31	chr11:85958400-85963800	Weak transcription	Fetal Intestine Small	intestine
32	chr11:85958400-85963800	Weak transcription	Fetal Stomach	stomach
33	chr11:85958400-85966200	Weak transcription	NH-A	brain
34	chr11:85958400-85966400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr11:85958400-85972400	Weak transcription	Aorta	Aorta
36	chr11:85958400-85997200	Weak transcription	Brain Germinal Matrix	brain
37	chr11:85958800-85961200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr11:85958800-85961400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:85958800-85961600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:85958800-85961600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:85958800-85967000	Weak transcription	HSMM	muscle
42	chr11:85959200-85961200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr11:85959200-85961200	Weak transcription	Fetal Lung	lung
44	chr11:85959200-85961200	Enhancers	A549	lung
45	chr11:85959200-85961200	Enhancers	NHEK	skin
46	chr11:85959200-85961400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:85959200-85961400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:85959200-85962200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:85959200-85963800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:85959200-85963800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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