Variant report

Variant	rs6717713
Chromosome Location	chr2:54735637-54735638
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	chr2:54735530..54737587-chr2:54805600..54807327,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1112919	0.80[EUR][1000 genomes]
rs12477376	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622708	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13387476	0.81[EUR][1000 genomes]
rs17045941	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519565	0.83[EUR][1000 genomes]
rs4671223	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671224	0.82[ASN][1000 genomes]
rs4671952	0.82[EUR][1000 genomes]
rs6545428	0.83[EUR][1000 genomes]
rs6717816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68134840	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309255	0.81[EUR][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	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6717713	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54712400-54737000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
3	chr2:54725200-54737600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
6	chr2:54727600-54737800	Weak transcription	A549	lung
7	chr2:54728000-54737400	Weak transcription	HSMM	muscle
8	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
9	chr2:54730200-54736800	Weak transcription	Placenta	Placenta
10	chr2:54730400-54736800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:54730600-54736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:54730600-54739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:54730600-54739200	Weak transcription	Spleen	Spleen
15	chr2:54730600-54739400	Weak transcription	HepG2	liver
16	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:54730800-54736800	Weak transcription	Fetal Brain Male	brain
18	chr2:54730800-54738600	Enhancers	Fetal Lung	lung
19	chr2:54731200-54737400	Weak transcription	Fetal Stomach	stomach
20	chr2:54731400-54736200	Weak transcription	Psoas Muscle	Psoas
21	chr2:54731400-54736600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:54731600-54735800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:54732400-54736600	Weak transcription	HSMMtube	muscle
24	chr2:54732400-54737400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54732600-54737400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:54732600-54738200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:54732800-54735800	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:54732800-54735800	Weak transcription	Brain Substantia Nigra	brain
29	chr2:54732800-54736800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:54732800-54736800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:54732800-54736800	Weak transcription	Liver	Liver
32	chr2:54732800-54736800	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:54732800-54736800	Weak transcription	NHDF-Ad	bronchial
34	chr2:54732800-54737400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:54732800-54737400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:54732800-54737600	Weak transcription	NHLF	lung
37	chr2:54732800-54740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
39	chr2:54733000-54735800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:54733000-54736800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
42	chr2:54733400-54736600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:54733600-54737000	Weak transcription	Lung	lung
44	chr2:54733600-54737400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:54733600-54747000	Weak transcription	Gastric	stomach
46	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:54734000-54736800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:54734600-54738400	Enhancers	Fetal Heart	heart
49	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:54734800-54737400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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