Variant report

Variant	rs56314487
Chromosome Location	chr7:102535721-102535722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102526206..102528003-chr7:102535680..102538379,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10487281	1.00[ASN][1000 genomes]
rs10487284	1.00[ASN][1000 genomes]
rs11496066	1.00[ASN][1000 genomes]
rs12113073	1.00[ASN][1000 genomes]
rs17135875	1.00[ASN][1000 genomes]
rs17135913	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135916	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474893	1.00[ASN][1000 genomes]
rs2041094	1.00[ASN][1000 genomes]
rs2228687	0.87[EUR][1000 genomes]
rs2411061	0.88[EUR][1000 genomes]
rs3893651	1.00[ASN][1000 genomes]
rs4377880	1.00[ASN][1000 genomes]
rs4398822	1.00[ASN][1000 genomes]
rs55681588	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781834	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849741	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55851590	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56336567	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56692051	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465886	0.84[EUR][1000 genomes]
rs66712128	0.87[EUR][1000 genomes]
rs6955064	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964296	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968036	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727175	1.00[ASN][1000 genomes]
rs73192015	1.00[ASN][1000 genomes]
rs73192019	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192025	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73192026	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73714541	0.87[EUR][1000 genomes]
rs7779854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781557	1.00[ASN][1000 genomes]
rs7798582	0.87[EUR][1000 genomes]
rs7809047	1.00[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	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
10	nsv5880	chr7:102505158-102550471	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56314487	LRRC17	cis	Stomach	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517000-102549600	Weak transcription	Gastric	stomach
2	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:102522600-102549200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:102532400-102535800	Weak transcription	Ovary	ovary
5	chr7:102532400-102535800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:102532400-102538000	Weak transcription	Stomach Mucosa	stomach
7	chr7:102532400-102538800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:102532400-102538800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:102532600-102536000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:102533400-102537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr7:102533600-102536800	Weak transcription	Fetal Kidney	kidney
12	chr7:102533600-102537200	Weak transcription	NHLF	lung
13	chr7:102533600-102537800	Weak transcription	Adipose Nuclei	Adipose
14	chr7:102533600-102537800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:102533800-102536000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:102533800-102537000	Weak transcription	NH-A	brain
17	chr7:102533800-102538000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:102533800-102538600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:102534000-102537400	Weak transcription	HUVEC	blood vessel
20	chr7:102534000-102537800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:102534000-102537800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:102534000-102538400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:102534000-102538800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:102534600-102535800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:102534600-102536600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:102534600-102537600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:102534800-102536000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:102534800-102536800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr7:102535000-102536000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:102535000-102536000	Weak transcription	HSMM	muscle
31	chr7:102535400-102536000	Weak transcription	NHDF-Ad	bronchial
32	chr7:102535400-102536200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:102535400-102537400	Strong transcription	K562	blood
34	chr7:102535600-102535800	Enhancers	Fetal Muscle Leg	muscle
35	chr7:102535600-102536200	Enhancers	Right Atrium	heart
36	chr7:102535600-102536600	Enhancers	Aorta	Aorta
37	chr7:102535600-102537400	Enhancers	Rectal Smooth Muscle	rectum
38	chr7:102535600-102538400	Enhancers	Colon Smooth Muscle	Colon
39	chr7:102535600-102539200	Enhancers	Fetal Lung	lung
40	chr7:102535600-102539200	Enhancers	Fetal Stomach	stomach

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