Variant report

Variant	rs11741906
Chromosome Location	chr5:178461594-178461595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178460496..178462361-chr5:178485766..178487782,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177932	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10464075	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249610	0.86[CEU][hapmap]
rs11739654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749528	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12188377	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17665945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56851632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73340570	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73340597	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7732931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11741906	NPFFR1	trans	cerebellum	SCAN
rs11741906	CDHR2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178451200-178461800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr5:178451400-178461800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:178451600-178461800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr5:178451800-178461800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:178451800-178461800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:178451800-178464000	ZNF genes & repeats	Liver	Liver
7	chr5:178453000-178461800	ZNF genes & repeats	Brain Anterior Caudate	brain
8	chr5:178453000-178464000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr5:178453200-178461800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr5:178453200-178461800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
11	chr5:178453200-178461800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:178453200-178461800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr5:178453200-178461800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr5:178453200-178462400	ZNF genes & repeats	Fetal Brain Female	brain
15	chr5:178453400-178461600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
16	chr5:178453600-178461600	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr5:178453600-178461600	ZNF genes & repeats	Brain Substantia Nigra	brain
18	chr5:178453600-178461800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr5:178453600-178462000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr5:178453600-178464200	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr5:178453600-178465800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr5:178453800-178461600	ZNF genes & repeats	Brain Angular Gyrus	brain
23	chr5:178453800-178461800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:178453800-178461800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
25	chr5:178453800-178461800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
26	chr5:178453800-178462800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:178454000-178461600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
28	chr5:178454000-178461600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
29	chr5:178454000-178461800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
30	chr5:178454000-178461800	ZNF genes & repeats	Colon Smooth Muscle	Colon
31	chr5:178454000-178461800	ZNF genes & repeats	Fetal Brain Male	brain
32	chr5:178454000-178461800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
33	chr5:178454000-178462000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr5:178454000-178462000	ZNF genes & repeats	Brain Hippocampus Middle	brain
35	chr5:178454200-178464000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:178454400-178461600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:178455000-178461600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:178455000-178461800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:178455200-178461800	ZNF genes & repeats	Fetal Heart	heart
40	chr5:178455200-178461800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr5:178455200-178461800	ZNF genes & repeats	Psoas Muscle	Psoas
42	chr5:178455800-178461800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
43	chr5:178456000-178461800	ZNF genes & repeats	Fetal Lung	lung
44	chr5:178456800-178461800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
45	chr5:178457200-178461600	ZNF genes & repeats	Left Ventricle	heart
46	chr5:178457400-178461600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
47	chr5:178457800-178461600	ZNF genes & repeats	HSMMtube	muscle
48	chr5:178457800-178461800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
49	chr5:178457800-178461800	ZNF genes & repeats	HSMM	muscle
50	chr5:178458000-178461600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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