Variant report

Variant	rs11542226
Chromosome Location	chr3:141464231-141464232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141460791..141464587-chr3:141594120..141597016,3	MCF-7	breast:
2	chr3:141460404..141464291-chr3:141593804..141597029,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1533501	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16851689	1.00[JPT][hapmap]
rs16851691	1.00[JPT][hapmap]
rs16851704	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16851717	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16851740	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16851752	0.83[EUR][1000 genomes]
rs17787772	0.82[JPT][hapmap]
rs1879284	0.85[EUR][1000 genomes]
rs1879285	0.85[EUR][1000 genomes]
rs1980192	0.85[EUR][1000 genomes]
rs2677426	0.82[JPT][hapmap]
rs3773840	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4538350	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4586785	1.00[JPT][hapmap]
rs4588340	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57983026	0.85[EUR][1000 genomes]
rs58115387	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58300294	0.83[EUR][1000 genomes]
rs59998648	0.89[AFR][1000 genomes]
rs60317930	0.86[EUR][1000 genomes]
rs60938827	0.83[EUR][1000 genomes]
rs61632965	0.89[AFR][1000 genomes]
rs6783647	0.85[EUR][1000 genomes]
rs6783736	0.85[EUR][1000 genomes]
rs6787712	0.84[EUR][1000 genomes]
rs72982481	0.83[EUR][1000 genomes]
rs73000336	0.83[EUR][1000 genomes]
rs7632069	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7642922	0.85[EUR][1000 genomes]
rs7643689	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789959	0.85[EUR][1000 genomes]
rs9789973	0.85[EUR][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11542226	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141458200-141470400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:141458600-141468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:141458800-141470800	Weak transcription	Stomach Mucosa	stomach
4	chr3:141459000-141465600	Weak transcription	Lung	lung
5	chr3:141459000-141465800	Weak transcription	Gastric	stomach
6	chr3:141459600-141470800	Weak transcription	Fetal Brain Male	brain
7	chr3:141460000-141467000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:141460200-141466000	Weak transcription	Ovary	ovary
9	chr3:141460200-141466400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:141460200-141468000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:141460200-141468200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:141460200-141469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:141460400-141465800	Weak transcription	Aorta	Aorta
14	chr3:141460400-141465800	Weak transcription	Psoas Muscle	Psoas
15	chr3:141460400-141466000	Weak transcription	Small Intestine	intestine
16	chr3:141460400-141472400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:141460800-141466000	Strong transcription	K562	blood
18	chr3:141460800-141470400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:141461000-141471600	Strong transcription	Fetal Thymus	thymus
20	chr3:141461200-141464600	Strong transcription	HSMM	muscle
21	chr3:141461200-141470000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:141461400-141466400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:141461400-141466800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:141461400-141467000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:141461400-141467200	Strong transcription	Osteobl	bone
26	chr3:141461400-141467600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:141461400-141469400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:141461400-141469600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:141461400-141469600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:141461400-141470000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:141461400-141470000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:141461400-141470000	Strong transcription	Placenta	Placenta
33	chr3:141461400-141471800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:141461600-141466600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr3:141461600-141467200	Strong transcription	NH-A	brain
36	chr3:141461600-141467400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:141461600-141471400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:141461800-141465800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:141461800-141467400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:141461800-141498200	Weak transcription	Right Ventricle	heart
41	chr3:141462000-141469800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:141462200-141464800	Strong transcription	NHEK	skin
43	chr3:141462200-141465800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:141462200-141467000	Strong transcription	Hela-S3	cervix
45	chr3:141462200-141467400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:141462200-141469600	Strong transcription	Dnd41	blood
47	chr3:141462200-141470800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:141462200-141473200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:141462400-141465200	Weak transcription	Fetal Lung	lung
50	chr3:141462400-141465400	Weak transcription	Fetal Heart	heart

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