Variant report

Variant	rs4140934
Chromosome Location	chr4:15490558-15490559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15479756..15482166-chr4:15489455..15493787,3	MCF-7	breast:
2	chr4:15484757..15487117-chr4:15489258..15491846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11728800	0.81[EUR][1000 genomes]
rs12500458	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs13131700	0.85[EUR][1000 genomes]
rs1861048	0.92[CEU][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2080176	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080177	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087622	0.84[EUR][1000 genomes]
rs34465372	0.85[EUR][1000 genomes]
rs4063953	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140933	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698112	0.83[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698386	0.80[AMR][1000 genomes]
rs4698387	0.85[EUR][1000 genomes]
rs6810461	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs719993	0.88[YRI][hapmap]
rs9990934	0.84[YRI][hapmap]
rs9993748	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998686	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998697	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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 target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4140934	CLRN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481600-15498600	Weak transcription	Liver	Liver
2	chr4:15481600-15519000	Weak transcription	Gastric	stomach
3	chr4:15482000-15491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:15482000-15491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:15482600-15516600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:15482600-15526400	Weak transcription	HMEC	breast
8	chr4:15482800-15518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:15483600-15493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:15483600-15498600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:15485000-15504800	Weak transcription	Ovary	ovary
12	chr4:15485200-15494400	Weak transcription	Fetal Heart	heart
13	chr4:15486600-15499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:15487200-15498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
16	chr4:15488600-15491000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:15488800-15492200	ZNF genes & repeats	Fetal Lung	lung
18	chr4:15489800-15491000	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr4:15489800-15493000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr4:15490000-15490600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:15490000-15490600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:15490000-15490600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:15490000-15491000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
24	chr4:15490000-15491200	Genic enhancers	Osteobl	bone
25	chr4:15490000-15491600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr4:15490200-15490600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:15490200-15490600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:15490200-15490600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr4:15490200-15490600	ZNF genes & repeats	Aorta	Aorta
30	chr4:15490200-15490600	ZNF genes & repeats	Fetal Brain Female	brain
31	chr4:15490200-15490600	ZNF genes & repeats	Fetal Stomach	stomach
32	chr4:15490200-15490600	ZNF genes & repeats	Left Ventricle	heart
33	chr4:15490200-15490600	ZNF genes & repeats	Lung	lung
34	chr4:15490200-15490600	Flanking Active TSS	NHLF	lung
35	chr4:15490200-15490800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:15490200-15490800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:15490200-15490800	ZNF genes & repeats	Colon Smooth Muscle	Colon
38	chr4:15490200-15491000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr4:15490200-15491000	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr4:15490200-15491600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:15490200-15491600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr4:15490200-15491600	Enhancers	NHDF-Ad	bronchial
43	chr4:15490200-15494200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:15490200-15498400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:15490400-15490600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:15490400-15490600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
47	chr4:15490400-15490600	ZNF genes & repeats	A549	lung
48	chr4:15490400-15490800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:15490400-15490800	Strong transcription	Fetal Kidney	kidney
50	chr4:15490400-15492000	Weak transcription	Pancreas	Pancrea

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