Variant report

Variant	rs340121
Chromosome Location	chr5:178688093-178688094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178688082..178688899-chr5:178920410..178921212,2	MCF-7	breast:
2	chr5:178570556..178571105-chr5:178687987..178688905,2	MCF-7	breast:
3	chr5:178570203..178571201-chr5:178687913..178688718,3	MCF-7	breast:
4	chr5:178593807..178594987-chr5:178687910..178688845,5	MCF-7	breast:
5	chr5:178219952..178220766-chr5:178688074..178688887,3	MCF-7	breast:
6	chr5:178639654..178640533-chr5:178687929..178688900,5	MCF-7	breast:
7	chr5:178687965..178688655-chr5:178920708..178921301,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17079267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17079284	0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs72818696	0.98[ASN][1000 genomes]
rs9885424	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1016097	chr5:178544084-178866001	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1026968	chr5:178545479-178865895	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv537976	chr5:178545479-178865895	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv600496	chr5:178552518-178752351	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv883228	chr5:178604465-178796142	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv883231	chr5:178614867-178813207	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv830558	chr5:178624391-178805604	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv883232	chr5:178626437-178805612	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1018641	chr5:178627012-178911254	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv537978	chr5:178627012-178911254	Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv462576	chr5:178645310-178698709	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv600498	chr5:178645310-178698709	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv462577	chr5:178645310-178706162	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv600499	chr5:178645310-178706162	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv462578	chr5:178659691-178713712	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv600500	chr5:178659691-178713712	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
23	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
24	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
25	nsv883233	chr5:178675065-178746447	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv883234	chr5:178686438-178728830	Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340121	CDHR2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178670000-178691800	Weak transcription	Right Atrium	heart
2	chr5:178684200-178688200	Weak transcription	Placenta	Placenta
3	chr5:178684600-178691000	Weak transcription	NHDF-Ad	bronchial
4	chr5:178685400-178690600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:178685800-178689200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr5:178685800-178691800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:178686800-178688600	Weak transcription	Spleen	Spleen
8	chr5:178686800-178691600	Weak transcription	Fetal Lung	lung
9	chr5:178686800-178691800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:178686800-178691800	Weak transcription	Gastric	stomach
11	chr5:178687000-178688400	Genic enhancers	Fetal Stomach	stomach
12	chr5:178687000-178688600	Weak transcription	Lung	lung
13	chr5:178687200-178688600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:178687200-178688600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:178687200-178690600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:178687200-178691800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:178687400-178688200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:178687400-178691400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:178687400-178691400	Weak transcription	NHLF	lung
20	chr5:178687600-178689200	Enhancers	Fetal Muscle Leg	muscle
21	chr5:178687600-178691000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:178687800-178688200	Strong transcription	Osteobl	bone
23	chr5:178687800-178689000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr5:178688000-178688200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:178688000-178688800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:178688000-178688800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr5:178688000-178688800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:178688000-178688800	Enhancers	HSMMtube	muscle
29	chr5:178688000-178689000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:178688000-178689000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:178688000-178689000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr5:178688000-178689200	Enhancers	HSMM	muscle
33	chr5:178688000-178689400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:178688000-178689400	Enhancers	HepG2	liver
35	chr5:178688000-178690600	Weak transcription	Adipose Nuclei	Adipose
36	chr5:178688000-178691600	Weak transcription	Ovary	ovary

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