Variant report

Variant	rs3923738
Chromosome Location	chr11:85959831-85959832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85957956..85960491-chr11:85965054..85967049,2	K562	blood:
2	chr11:85958310..85960739-chr11:85984735..85987503,2	MCF-7	breast:
3	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: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10792840	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898450	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898455	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898456	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234583	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11234585	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11234586	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11234587	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234591	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234592	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234595	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1215001	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12225782	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12226796	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12282663	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574118	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577739	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12800606	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376947	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391221	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs19039	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291225	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs291227	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291228	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291230	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291231	0.87[EUR][1000 genomes]
rs291232	0.87[EUR][1000 genomes]
rs291233	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291234	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291235	0.88[EUR][1000 genomes]
rs291236	0.85[EUR][1000 genomes]
rs291237	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291238	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291242	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs291247	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs291251	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34095340	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34972740	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4547120	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944562	0.86[AFR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3923738	EED	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr11:85957400-85960000	Enhancers	Small Intestine	intestine
8	chr11:85957400-85961400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr11:85957400-85961600	Enhancers	Primary B cells from peripheral blood	blood
10	chr11:85957400-85962400	Weak transcription	Placenta	Placenta
11	chr11:85957400-85967600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:85957400-85985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
14	chr11:85957600-85961200	Enhancers	Primary T cells from cord blood	blood
15	chr11:85957600-85961600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr11:85957800-85960000	Enhancers	Adipose Nuclei	Adipose
17	chr11:85957800-85960200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:85957800-85960600	Weak transcription	Brain Hippocampus Middle	brain
19	chr11:85957800-85960800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:85957800-85961600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr11:85957800-85962000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr11:85957800-85962600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:85957800-85962800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:85957800-85967800	Weak transcription	Thymus	Thymus
25	chr11:85957800-85968000	Weak transcription	HSMMtube	muscle
26	chr11:85957800-85968600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:85957800-85968600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:85957800-85997200	Weak transcription	Colonic Mucosa	Colon
29	chr11:85957800-85999800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:85958000-85960000	Enhancers	Fetal Brain Female	brain
31	chr11:85958000-85960400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr11:85958000-85960800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:85958000-85961000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:85958000-85961000	Weak transcription	Brain Substantia Nigra	brain
35	chr11:85958000-85961000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr11:85958000-85961600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr11:85958000-85963400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:85958200-85960000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:85958200-85960000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr11:85958200-85960800	Weak transcription	Primary B cells from cord blood	blood
41	chr11:85958200-85962400	Weak transcription	Osteobl	bone
42	chr11:85958400-85960600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:85958400-85960600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:85958400-85961000	Enhancers	Stomach Mucosa	stomach
45	chr11:85958400-85961200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:85958400-85961600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr11:85958400-85962200	Weak transcription	Fetal Thymus	thymus
48	chr11:85958400-85963800	Weak transcription	Fetal Intestine Small	intestine
49	chr11:85958400-85963800	Weak transcription	Fetal Stomach	stomach
50	chr11:85958400-85966200	Weak transcription	NH-A	brain

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