Variant report

Variant	rs10220027
Chromosome Location	chr13:111173659-111173660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111155981..111156623-chr13:111173427..111174132,2	NB4	blood:
2	chr13:111173040..111177244-chr13:111365856..111368723,3	MCF-7	breast:
3	chr13:111171438..111174386-chr13:111180872..111182991,2	MCF-7	breast:
4	chr13:111162545..111165671-chr13:111172658..111175880,3	MCF-7	breast:
5	chr13:111171406..111173667-chr13:111365704..111368151,2	K562	blood:

Variant related genes	Relation type
ENSG00000134905	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10047685	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1059289	0.93[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296846	0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3742190	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv901009	chr13:111134780-111176393	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv984479	chr13:111157297-111176429	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a
10	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
11	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
12	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
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10220027	LAMP1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111155200-111175600	Weak transcription	Fetal Thymus	thymus
2	chr13:111159600-111176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:111160800-111176400	Weak transcription	Psoas Muscle	Psoas
4	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr13:111162600-111177200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:111163200-111175400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:111165400-111179800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:111165600-111175600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:111165600-111176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:111165600-111176600	Weak transcription	HMEC	breast
11	chr13:111165800-111179400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr13:111166600-111176800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:111166800-111175600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr13:111167000-111190800	Weak transcription	Fetal Kidney	kidney
15	chr13:111167200-111179600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr13:111167400-111176800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:111167600-111174400	Weak transcription	Aorta	Aorta
18	chr13:111169600-111174800	Genic enhancers	Fetal Intestine Small	intestine
19	chr13:111169600-111178600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr13:111170000-111175200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr13:111170200-111175000	Enhancers	Fetal Muscle Leg	muscle
22	chr13:111170800-111175200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr13:111171200-111175000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:111171400-111173800	Weak transcription	Small Intestine	intestine
25	chr13:111171400-111174400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:111171400-111176200	Weak transcription	Hela-S3	cervix
27	chr13:111171400-111176600	Weak transcription	K562	blood
28	chr13:111171400-111178200	Enhancers	Fetal Brain Male	brain
29	chr13:111171600-111174000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:111171800-111174000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:111171800-111175000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:111172000-111175000	Enhancers	Fetal Muscle Trunk	muscle
33	chr13:111172200-111175200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr13:111172200-111175400	Enhancers	Adipose Nuclei	Adipose
35	chr13:111172200-111176200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:111172400-111174000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:111172400-111174600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:111172400-111174600	Enhancers	Spleen	Spleen
39	chr13:111172400-111175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr13:111172600-111174600	Enhancers	NHDF-Ad	bronchial
41	chr13:111172600-111175600	Enhancers	Placenta	Placenta
42	chr13:111172800-111173800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:111172800-111173800	Enhancers	HSMMtube	muscle
44	chr13:111172800-111174000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr13:111172800-111174000	Enhancers	Lung	lung
46	chr13:111172800-111174000	Enhancers	HSMM	muscle
47	chr13:111172800-111174400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr13:111172800-111174600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:111172800-111174600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr13:111172800-111174600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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