Variant report

Variant	rs6578398
Chromosome Location	chr11:3638061-3638062
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	chr11:3628892..3631484-chr11:3636382..3639182,2	K562	blood:

Variant related genes	Relation type
ENSG00000182048	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2203402	0.95[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2203403	0.86[GIH][hapmap]
rs2221992	0.82[CEU][hapmap];0.92[GIH][hapmap];0.80[EUR][1000 genomes]
rs4432051	0.95[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs6578394	0.81[EUR][1000 genomes]
rs6578395	0.81[EUR][1000 genomes]
rs6578397	0.86[GIH][hapmap]
rs6578400	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111164	0.84[GIH][hapmap]
rs7929578	0.87[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7946339	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047763	chr11:2918998-3751029	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	esv2758252	chr11:3236512-3801429	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2759796	chr11:3236512-3801429	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2760300	chr11:3416489-3667988	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	esv18699	chr11:3426081-3674989	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv832051	chr11:3523947-3728714	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv467660	chr11:3568044-3660914	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv553140	chr11:3568044-3660914	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1820972	chr11:3616884-3801429	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	esv1821329	chr11:3616884-3801429	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv832052	chr11:3616884-3801429	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv428247	chr11:3616884-3801429	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv526441	chr11:3626177-3756686	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv976446	chr11:3626480-3648596	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1046356	chr11:3628837-3774215	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	nsv1044345	chr11:3628912-3739222	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	nsv540906	chr11:3628912-3739222	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
18	nsv1044419	chr11:3628912-3751029	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv896892	chr11:3632107-3654676	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1045810	chr11:3635610-3657520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1052573	chr11:3637802-3665561	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6578398	PLA2G2C	trans	cerebellum	SCAN
rs6578398	CEND1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3635000-3639200	Enhancers	Fetal Muscle Leg	muscle
2	chr11:3635400-3638200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:3635400-3638400	Enhancers	HSMMtube	muscle
4	chr11:3636000-3638200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:3636000-3639800	Weak transcription	Thymus	Thymus
6	chr11:3636000-3648400	Weak transcription	Right Atrium	heart
7	chr11:3636400-3646800	Weak transcription	Spleen	Spleen
8	chr11:3636600-3638400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr11:3636800-3638200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:3637000-3638200	Enhancers	HMEC	breast
11	chr11:3637000-3639400	Weak transcription	GM12878-XiMat	blood
12	chr11:3637200-3638200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:3637200-3638200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr11:3637200-3638800	Enhancers	Fetal Muscle Trunk	muscle
15	chr11:3637400-3638200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:3637400-3638400	Enhancers	Ovary	ovary
17	chr11:3637800-3638200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:3637800-3638200	Weak transcription	Placenta	Placenta
19	chr11:3637800-3638200	Enhancers	Fetal Thymus	thymus
20	chr11:3637800-3638400	Enhancers	HSMM	muscle
21	chr11:3637800-3638600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:3637800-3638600	Bivalent Enhancer	Fetal Stomach	stomach
23	chr11:3638000-3638200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:3638000-3638200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:3638000-3638200	Enhancers	Esophagus	oesophagus
26	chr11:3638000-3638200	Enhancers	Right Ventricle	heart
27	chr11:3638000-3638400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr11:3638000-3638600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:3638000-3638800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:3638000-3639600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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