Variant report

Variant	rs35399723
Chromosome Location	chr7:102973794-102973795
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102973791..102979614-chr7:102983161..102986751,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105821	Chromatin interaction
ENSG00000161057	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10245155	0.97[ASN][1000 genomes]
rs10266523	1.00[ASN][1000 genomes]
rs17680523	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2878	0.93[ASN][1000 genomes]
rs3087615	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4729911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62482370	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62482394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482396	0.97[ASN][1000 genomes]
rs62482397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482403	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482404	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482406	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6971734	0.97[ASN][1000 genomes]
rs73175837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73175852	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35399723	RP11-401L13.5	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102938600-102984200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:102939800-102980800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:102939800-102984000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:102939800-102984200	Weak transcription	Stomach Mucosa	stomach
5	chr7:102940000-102983000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:102948800-102982600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr7:102952000-102983800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:102954600-102984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:102957400-102977000	Weak transcription	Fetal Brain Male	brain
10	chr7:102959400-102977000	Weak transcription	Colonic Mucosa	Colon
11	chr7:102959600-102974600	Weak transcription	Esophagus	oesophagus
12	chr7:102959600-102981200	Weak transcription	Pancreas	Pancrea
13	chr7:102960200-102981000	Weak transcription	Fetal Heart	heart
14	chr7:102960400-102984200	Weak transcription	Spleen	Spleen
15	chr7:102960600-102976400	Weak transcription	Small Intestine	intestine
16	chr7:102960600-102977400	Weak transcription	Brain Angular Gyrus	brain
17	chr7:102960800-102977400	Weak transcription	Psoas Muscle	Psoas
18	chr7:102961000-102975400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:102961800-102975800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:102962400-102977200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:102962400-102977400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:102962400-102981400	Weak transcription	Gastric	stomach
23	chr7:102962400-102984200	Weak transcription	Aorta	Aorta
24	chr7:102963200-102977000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:102964600-102976000	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:102964800-102977200	Strong transcription	Fetal Intestine Small	intestine
27	chr7:102965600-102974800	Weak transcription	Fetal Lung	lung
28	chr7:102965600-102975200	Weak transcription	Fetal Brain Female	brain
29	chr7:102965600-102977200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:102965600-102977400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:102965800-102974000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:102965800-102976800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:102965800-102977000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:102966000-102977400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:102966000-102981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:102966200-102973800	Weak transcription	HSMMtube	muscle
37	chr7:102966400-102977400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:102966600-102976000	Weak transcription	Ovary	ovary
39	chr7:102966600-102977000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:102966800-102974400	Weak transcription	Lung	lung
41	chr7:102966800-102976200	Weak transcription	Brain Germinal Matrix	brain
42	chr7:102966800-102976800	Weak transcription	Brain Substantia Nigra	brain
43	chr7:102967000-102975200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr7:102967000-102980800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:102967200-102976600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:102967600-102975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:102967600-102977400	Weak transcription	NHLF	lung
48	chr7:102967800-102977000	Weak transcription	HMEC	breast
49	chr7:102968000-102974000	Weak transcription	NHEK	skin
50	chr7:102968000-102974600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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