Variant report

Variant	rs330554
Chromosome Location	chr13:111265178-111265179
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	chr13:111213298..111215293-chr13:111263862..111265630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139832	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2765346	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2766501	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2986321	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330550	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs330556	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs330558	0.94[ASN][1000 genomes]
rs330563	0.80[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs330564	0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs330566	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs392660	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs403908	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441805	0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61970485	0.93[EUR][1000 genomes]
rs7394	0.85[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7998306	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS 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	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS 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 lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
13	nsv1038089	chr13:111229517-111274823	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
14	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
15	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs330554	AL139385.1	cis	Muscle Skeletal	GTEx
rs330554	CARKD	cis	Whole Blood	GTEx
rs330554	CARKD	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111262600-111265200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr13:111262600-111267200	Weak transcription	HSMM	muscle
3	chr13:111263000-111267000	Weak transcription	Esophagus	oesophagus
4	chr13:111263000-111267200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:111263000-111267200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:111263000-111267400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr13:111263000-111267400	Weak transcription	Fetal Kidney	kidney
8	chr13:111263200-111267200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:111263200-111267400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:111263400-111267200	Weak transcription	Placenta	Placenta
11	chr13:111263400-111267400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:111263600-111267400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr13:111263800-111267600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:111264000-111267000	Weak transcription	Hela-S3	cervix
15	chr13:111264000-111267200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:111264000-111267200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr13:111264000-111267200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr13:111264000-111267400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:111264000-111267400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:111264200-111267200	Weak transcription	NHEK	skin
21	chr13:111264200-111267400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr13:111264200-111267400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr13:111264200-111267400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr13:111264400-111267000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr13:111264400-111267200	Weak transcription	Brain Anterior Caudate	brain
26	chr13:111264400-111267200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr13:111264400-111267400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:111264600-111267000	Weak transcription	GM12878-XiMat	blood

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