Variant report

Variant	rs3825022
Chromosome Location	chr11:67013197-67013198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66823467..66825638-chr11:67011327..67013483,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173156	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10400320	1.00[EUR][1000 genomes]
rs10732253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750796	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896171	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11227699	1.00[GIH][hapmap]
rs11227771	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11227780	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1253784	1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1894111	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2255990	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs3741189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815364	1.00[CHB][hapmap]
rs4271388	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4344498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457752	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57327069	1.00[EUR][1000 genomes]
rs57478329	0.81[EUR][1000 genomes]
rs57724865	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58224869	1.00[EUR][1000 genomes]
rs59057433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59817822	0.94[EUR][1000 genomes]
rs61180657	0.82[ASN][1000 genomes]
rs61663253	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655168	1.00[EUR][1000 genomes]
rs682509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7937611	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7941655	0.89[JPT][hapmap]

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	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv933183	chr11:67008447-67160993	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3825022	RPS6KB2	cis	multi-tissue	Pritchard
rs3825022	RPS6KB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67009200-67028800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:67009600-67025400	Strong transcription	Fetal Thymus	thymus
3	chr11:67010000-67015400	Strong transcription	NHLF	lung
4	chr11:67010000-67018400	Genic enhancers	Placenta	Placenta
5	chr11:67010000-67020200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr11:67010000-67025000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:67010000-67026600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:67010200-67014200	Strong transcription	NHDF-Ad	bronchial
9	chr11:67010200-67015000	Strong transcription	Lung	lung
10	chr11:67010200-67018800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:67010200-67024400	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr11:67010200-67024600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:67010200-67025000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:67010200-67025000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:67010200-67025000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:67010200-67025000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:67010200-67025400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr11:67010200-67025400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:67010200-67025800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr11:67010200-67026600	Strong transcription	Fetal Stomach	stomach
21	chr11:67010400-67015200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:67010400-67019000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr11:67010400-67020200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:67010400-67024600	Strong transcription	HUVEC	blood vessel
25	chr11:67010400-67025000	Strong transcription	Fetal Brain Female	brain
26	chr11:67010400-67025000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:67010400-67025000	Strong transcription	Thymus	Thymus
28	chr11:67010400-67025000	Strong transcription	NH-A	brain
29	chr11:67010400-67026200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:67010600-67013800	Strong transcription	NHEK	skin
31	chr11:67010600-67014600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:67010600-67015000	Strong transcription	A549	lung
33	chr11:67010600-67015200	Strong transcription	HSMM	muscle
34	chr11:67010600-67015400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr11:67010600-67015400	Strong transcription	HSMMtube	muscle
36	chr11:67010600-67015600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:67010600-67015800	Weak transcription	Right Atrium	heart
38	chr11:67010600-67016000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:67010600-67018200	Strong transcription	K562	blood
40	chr11:67010600-67018400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:67010600-67019600	Strong transcription	Primary T cells from cord blood	blood
42	chr11:67010600-67020000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:67010600-67020000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr11:67010600-67020200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:67010600-67020400	Strong transcription	Fetal Intestine Small	intestine
46	chr11:67010600-67024400	Strong transcription	Psoas Muscle	Psoas
47	chr11:67010600-67024800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:67010600-67025000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr11:67010600-67025000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:67010600-67025000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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