Variant report

Variant	rs12214968
Chromosome Location	chr6:5494234-5494235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10223437	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10223725	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11755552	1.00[CHB][hapmap]
rs12211013	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211016	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12211019	1.00[ASN][1000 genomes]
rs12211052	1.00[ASN][1000 genomes]
rs12212484	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12213351	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34454236	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34670959	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35304975	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs395378	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs395394	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs408705	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs409548	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs448138	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs9504412	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9504413	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.95[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	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12214968	PRPF4B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5449000-5499400	Weak transcription	Fetal Intestine Large	intestine
2	chr6:5461600-5507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:5466400-5518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr6:5466600-5506400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:5466800-5502200	Weak transcription	Gastric	stomach
6	chr6:5471800-5505800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:5472400-5511600	Weak transcription	Fetal Stomach	stomach
8	chr6:5472600-5496800	Weak transcription	NHDF-Ad	bronchial
9	chr6:5472600-5499400	Weak transcription	Spleen	Spleen
10	chr6:5472600-5501800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:5472600-5506200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:5481400-5497600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:5481600-5496000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:5481600-5496800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:5481600-5499400	Weak transcription	Right Ventricle	heart
16	chr6:5481600-5499600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:5481600-5500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:5482000-5499600	Weak transcription	Brain Anterior Caudate	brain
19	chr6:5482200-5498200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:5482200-5506600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:5483400-5500600	Weak transcription	Pancreas	Pancrea
22	chr6:5485000-5500200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:5485200-5506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:5485800-5496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:5486000-5505400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:5486200-5498400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:5486200-5506800	Weak transcription	Thymus	Thymus
28	chr6:5486400-5502800	Weak transcription	HepG2	liver
29	chr6:5487000-5498600	Weak transcription	HMEC	breast
30	chr6:5487000-5499000	Weak transcription	NHEK	skin
31	chr6:5487000-5499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:5487200-5494800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:5487200-5499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:5488000-5497600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:5488000-5501800	Weak transcription	Liver	Liver
36	chr6:5488000-5510600	Weak transcription	Aorta	Aorta
37	chr6:5488200-5496600	Weak transcription	Adipose Nuclei	Adipose
38	chr6:5488200-5498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:5488200-5498800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr6:5488200-5506200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:5488200-5506400	Weak transcription	Fetal Intestine Small	intestine
42	chr6:5488600-5506000	Weak transcription	Primary B cells from cord blood	blood
43	chr6:5488600-5521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:5491000-5495400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:5491200-5496800	Weak transcription	Brain Germinal Matrix	brain
46	chr6:5492200-5499800	Weak transcription	Primary T cells from cord blood	blood
47	chr6:5493000-5494800	Enhancers	Psoas Muscle	Psoas
48	chr6:5493800-5494400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr6:5494000-5494400	Weak transcription	Left Ventricle	heart
50	chr6:5494200-5499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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