Variant report

Variant	rs1880272
Chromosome Location	chr6:25354218-25354219
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	chr6:25279234..25281745-chr6:25353189..25355641,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10946764	0.86[ASN][1000 genomes]
rs10946765	0.86[ASN][1000 genomes]
rs11757140	0.80[EUR][1000 genomes]
rs13215347	0.82[ASN][1000 genomes]
rs186207	0.81[EUR][1000 genomes]
rs215012	0.85[EUR][1000 genomes]
rs215015	0.81[EUR][1000 genomes]
rs2690095	0.86[ASN][1000 genomes]
rs2744235	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744236	0.85[ASN][1000 genomes]
rs4712919	0.86[ASN][1000 genomes]
rs4712920	0.86[ASN][1000 genomes]
rs6933419	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880272	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25336800-25354600	Weak transcription	Right Atrium	heart
3	chr6:25337400-25357800	Weak transcription	NHEK	skin
4	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
5	chr6:25342800-25354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:25346600-25359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:25346800-25359200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:25347000-25359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:25349200-25359200	Weak transcription	Ovary	ovary
10	chr6:25350400-25355200	Enhancers	Fetal Lung	lung
11	chr6:25350600-25356000	Enhancers	Fetal Intestine Large	intestine
12	chr6:25350800-25359200	Weak transcription	Lung	lung
13	chr6:25351000-25359600	Weak transcription	Brain Anterior Caudate	brain
14	chr6:25351200-25354400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:25351200-25357400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:25351400-25354600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:25351800-25359200	Weak transcription	HSMMtube	muscle
18	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:25353000-25359400	Weak transcription	Fetal Thymus	thymus
20	chr6:25353200-25359600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:25353200-25359600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:25353400-25354600	Weak transcription	Fetal Intestine Small	intestine
23	chr6:25353400-25358200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:25353400-25358800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:25353400-25359200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:25353400-25359200	Weak transcription	Small Intestine	intestine
27	chr6:25353800-25357400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:25353800-25359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:25354000-25354400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:25354000-25354400	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr6:25354000-25354600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:25354000-25354600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr6:25354200-25355400	Enhancers	Fetal Heart	heart
34	chr6:25354200-25355400	Enhancers	Stomach Mucosa	stomach
35	chr6:25354200-25355800	Enhancers	Aorta	Aorta

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