Variant report

Variant	rs4910577
Chromosome Location	chr11:3847750-3847751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3845997..3848150-chr11:3857306..3860056,2	MCF-7	breast:
2	chr11:3846755..3850440-chr11:4090727..4095329,4	K562	blood:
3	chr11:3844970..3847923-chr11:3859030..3861537,2	MCF-7	breast:
4	chr11:3844575..3846833-chr11:3846927..3849386,4	MCF-7	breast:
5	chr11:3816391..3818213-chr11:3846207..3848807,2	K562	blood:

Variant related genes	Relation type
ENSG00000148985	Chromatin interaction
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1049388	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029983	1.00[ASN][1000 genomes]
rs11030043	0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs11030044	1.00[ASN][1000 genomes]
rs11030055	1.00[ASN][1000 genomes]
rs11030173	1.00[ASN][1000 genomes]
rs11600857	1.00[ASN][1000 genomes]
rs11606318	1.00[ASN][1000 genomes]
rs11606483	1.00[ASN][1000 genomes]
rs17173882	1.00[ASN][1000 genomes]
rs17191448	1.00[ASN][1000 genomes]
rs17276405	1.00[ASN][1000 genomes]
rs17276453	1.00[ASN][1000 genomes]
rs4367942	0.85[GIH][hapmap]
rs4910846	1.00[ASN][1000 genomes]
rs4910852	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910856	1.00[ASN][1000 genomes]
rs4910857	1.00[ASN][1000 genomes]
rs61896929	1.00[ASN][1000 genomes]
rs61896930	1.00[ASN][1000 genomes]
rs61896931	1.00[ASN][1000 genomes]
rs61896953	1.00[ASN][1000 genomes]
rs61896954	1.00[ASN][1000 genomes]
rs61896956	1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896958	1.00[ASN][1000 genomes]
rs61896959	1.00[ASN][1000 genomes]
rs61899361	1.00[ASN][1000 genomes]
rs61899362	1.00[ASN][1000 genomes]
rs61899363	1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs6578414	1.00[ASN][1000 genomes]
rs7101788	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs72844340	1.00[ASN][1000 genomes]
rs72844341	1.00[ASN][1000 genomes]
rs73430467	1.00[ASN][1000 genomes]
rs74050940	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1044360	chr11:3832288-3860024	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4910577	TRIM22	cis	cerebellum	SCAN
rs4910577	OR56A5	cis	parietal	SCAN
rs4910577	SLC22A18AS	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3830200-3852400	Weak transcription	Fetal Brain Male	brain
2	chr11:3830600-3848000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:3830600-3861000	Weak transcription	Fetal Kidney	kidney
4	chr11:3831200-3847800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:3832600-3853000	Weak transcription	Psoas Muscle	Psoas
6	chr11:3832800-3847800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:3842000-3853600	Strong transcription	Fetal Intestine Small	intestine
8	chr11:3842800-3848000	Weak transcription	Aorta	Aorta
9	chr11:3844000-3848600	Enhancers	Brain Angular Gyrus	brain
10	chr11:3844000-3857000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:3844400-3847800	Weak transcription	Ovary	ovary
12	chr11:3844400-3856200	Strong transcription	Fetal Stomach	stomach
13	chr11:3844600-3848200	Enhancers	Brain Anterior Caudate	brain
14	chr11:3844600-3849400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:3844600-3849400	Strong transcription	Brain Germinal Matrix	brain
16	chr11:3844600-3852800	Strong transcription	Fetal Intestine Large	intestine
17	chr11:3844600-3853400	Strong transcription	Thymus	Thymus
18	chr11:3844800-3854800	Strong transcription	Dnd41	blood
19	chr11:3844800-3857000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:3845000-3848000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:3845000-3848800	Weak transcription	HSMMtube	muscle
22	chr11:3845000-3849400	Strong transcription	Fetal Brain Female	brain
23	chr11:3845000-3856000	Weak transcription	HUVEC	blood vessel
24	chr11:3845200-3847800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:3845200-3849600	Strong transcription	Pancreas	Pancrea
26	chr11:3845200-3849600	Strong transcription	NHLF	lung
27	chr11:3845200-3852200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:3845200-3855800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:3845400-3847800	Weak transcription	NHDF-Ad	bronchial
30	chr11:3845400-3848000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:3845400-3848000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:3845400-3854200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:3845400-3855000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:3845400-3855800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:3845600-3849400	Genic enhancers	Spleen	Spleen
36	chr11:3845600-3851800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:3845600-3855800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:3845800-3847800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr11:3845800-3848600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:3845800-3849800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr11:3846000-3847800	Enhancers	Brain Cingulate Gyrus	brain
42	chr11:3846000-3851800	Strong transcription	Fetal Lung	lung
43	chr11:3846000-3853800	Strong transcription	A549	lung
44	chr11:3846200-3848000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:3846200-3848400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:3846200-3848400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr11:3846200-3848400	Strong transcription	Gastric	stomach
48	chr11:3846200-3848600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr11:3846200-3849000	Genic enhancers	H9 Cell Line	embryonic stem cell
50	chr11:3846200-3849200	Genic enhancers	HUES6 Cell Line	embryonic stem cell

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