Variant report

Variant	rs353604
Chromosome Location	chr11:35105698-35105699
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35104262..35106718-chr11:35159601..35161198,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000026508	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2467600	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2732570	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs353586	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs353590	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353592	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353595	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353597	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353606	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs353607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs387619	0.84[AMR][1000 genomes]
rs4755390	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv430371	chr11:34975067-35111292	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv540999	chr11:35021936-35185471	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv541000	chr11:35053717-35185471	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv541002	chr11:35101282-35224624	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv975326	chr11:35103908-35125981	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs353604	EIF3M	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35097600-35106400	Enhancers	Primary B cells from peripheral blood	blood
2	chr11:35097800-35106600	Enhancers	Fetal Thymus	thymus
3	chr11:35103200-35106600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:35103200-35106800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr11:35103200-35107800	Enhancers	Adipose Nuclei	Adipose
6	chr11:35103200-35110600	Enhancers	Fetal Muscle Leg	muscle
7	chr11:35103400-35106600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr11:35103600-35106800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:35103600-35108400	Enhancers	Fetal Muscle Trunk	muscle
10	chr11:35103800-35105800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr11:35103800-35105800	Flanking Active TSS	GM12878-XiMat	blood
12	chr11:35103800-35106000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr11:35103800-35106000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr11:35103800-35106000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:35103800-35106200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:35103800-35106200	Enhancers	Fetal Intestine Large	intestine
17	chr11:35103800-35106200	Enhancers	Fetal Stomach	stomach
18	chr11:35103800-35106400	Enhancers	Dnd41	blood
19	chr11:35103800-35106600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:35103800-35106600	Enhancers	Primary hematopoietic stem cells	blood
21	chr11:35103800-35106600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr11:35104000-35105800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr11:35104000-35105800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr11:35104000-35106000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:35104000-35106200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:35104000-35106200	Enhancers	Thymus	Thymus
27	chr11:35104000-35110400	Enhancers	Psoas Muscle	Psoas
28	chr11:35104200-35105800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr11:35104200-35106000	Flanking Active TSS	A549	lung
30	chr11:35104200-35106400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:35104200-35106600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr11:35104200-35106800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:35104400-35105800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:35104400-35107800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:35104400-35108800	Weak transcription	HUVEC	blood vessel
36	chr11:35104600-35106000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr11:35104600-35106200	Enhancers	Primary B cells from cord blood	blood
38	chr11:35104600-35106200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:35104600-35106800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr11:35104600-35110000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:35104800-35106400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:35104800-35106400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:35104800-35106600	Enhancers	HSMM	muscle
44	chr11:35104800-35106600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr11:35104800-35106800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:35104800-35109200	Weak transcription	Aorta	Aorta
47	chr11:35104800-35109200	Weak transcription	Spleen	Spleen
48	chr11:35105000-35105800	Enhancers	Duodenum Mucosa	Duodenum
49	chr11:35105000-35106000	Enhancers	Fetal Brain Male	brain
50	chr11:35105000-35106600	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links