Variant report

Variant	rs4478996
Chromosome Location	chr11:66889558-66889559
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66885406..66887210-chr11:66888913..66890834,2	MCF-7	breast:
2	chr11:66812155..66813969-chr11:66888125..66890651,2	K562	blood:
3	chr11:66889491..66892272-chr11:66894214..66896649,2	MCF-7	breast:
4	chr11:66884916..66890908-chr11:67005112..67010354,8	MCF-7	breast:
5	chr11:66883623..66889678-chr11:67005085..67009894,16	K562	blood:
6	chr11:66888331..66890567-chr11:66897930..66899479,2	MCF-7	breast:
7	chr11:66887881..66889769-chr11:66929494..66931769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173120	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10791899	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10896154	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896167	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs11227756	1.00[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap]
rs1253778	0.87[AMR][1000 genomes]
rs12791853	0.83[GIH][hapmap]
rs2001635	0.92[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2001636	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071007	1.00[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs2298815	0.83[GIH][hapmap]
rs3737460	0.83[GIH][hapmap]
rs3781943	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs3927807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4244819	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[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]
rs4255546	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4375446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4503557	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4542419	1.00[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4930192	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs4930418	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs56337023	0.84[ASN][1000 genomes]
rs608273	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646834	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6591232	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6591239	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs660960	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs674499	1.00[ASW][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7113390	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7484186	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7930829	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9943601	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4478996	RPS6KB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66885000-66889600	Active TSS	Psoas Muscle	Psoas
2	chr11:66885000-66889800	Active TSS	Fetal Brain Female	brain
3	chr11:66885000-66889800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr11:66885200-66889600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:66885200-66889600	Active TSS	Ovary	ovary
6	chr11:66885200-66889800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr11:66885200-66889800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:66885200-66890000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr11:66885200-66890000	Active TSS	HSMM	muscle
10	chr11:66885200-66890400	Active TSS	Brain Germinal Matrix	brain
11	chr11:66885200-66890600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:66885400-66889600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr11:66885400-66889600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:66885400-66889600	Active TSS	Fetal Muscle Leg	muscle
15	chr11:66885400-66889800	Active TSS	Aorta	Aorta
16	chr11:66885600-66889600	Active TSS	NHDF-Ad	bronchial
17	chr11:66885600-66890000	Active TSS	HSMMtube	muscle
18	chr11:66886200-66889600	Active TSS	Thymus	Thymus
19	chr11:66886200-66889600	Active TSS	HMEC	breast
20	chr11:66886200-66889800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:66886200-66889800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:66886200-66889800	Active TSS	NHLF	lung
23	chr11:66886200-66890000	Active TSS	GM12878-XiMat	blood
24	chr11:66886600-66889600	Active TSS	Stomach Smooth Muscle	stomach
25	chr11:66887000-66889800	Active TSS	Right Atrium	heart
26	chr11:66887000-66890600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:66887600-66889800	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr11:66887600-66890000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:66887800-66889800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr11:66887800-66890000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:66887800-66899600	Weak transcription	Spleen	Spleen
32	chr11:66888000-66889600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr11:66888000-66889600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr11:66888000-66889800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr11:66888400-66889800	Flanking Active TSS	HUVEC	blood vessel
36	chr11:66888400-66890000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:66888400-66890000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:66888600-66889600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
39	chr11:66888600-66889600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr11:66888600-66889800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:66888600-66889800	Active TSS	HepG2	liver
42	chr11:66888600-66890600	Weak transcription	Pancreas	Pancrea
43	chr11:66888600-66892600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:66888600-66922600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:66888800-66889600	Weak transcription	Small Intestine	intestine
46	chr11:66888800-66889800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:66888800-66889800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr11:66888800-66889800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:66888800-66889800	Weak transcription	Esophagus	oesophagus
50	chr11:66888800-66889800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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