Variant report

Variant	rs4519565
Chromosome Location	chr2:54756086-54756087
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	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
2	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10165641	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052820	0.88[CEU][hapmap]
rs1112919	0.92[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs12463484	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12475598	0.81[EUR][1000 genomes]
rs12476489	0.82[EUR][1000 genomes]
rs12477376	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12622708	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13387476	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045941	0.81[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs17416284	0.88[CEU][hapmap]
rs3817163	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs4283459	0.83[EUR][1000 genomes]
rs4567979	0.86[EUR][1000 genomes]
rs4671223	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs4671224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671227	0.87[EUR][1000 genomes]
rs4671952	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671959	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671962	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671965	0.92[CEU][hapmap]
rs60294349	0.81[EUR][1000 genomes]
rs6545428	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545433	0.96[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs6705756	0.88[CEU][hapmap]
rs6717713	0.83[EUR][1000 genomes]
rs6717816	0.83[EUR][1000 genomes]
rs6738725	0.80[CEU][hapmap]
rs6739099	0.83[EUR][1000 genomes]
rs68134840	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309255	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	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
2	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
3	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
4	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv961776	chr2:54755470-54757189	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4519565	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
11	chr2:54750600-54757000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:54751000-54756800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:54752000-54756200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
20	chr2:54752000-54764600	Weak transcription	Gastric	stomach
21	chr2:54752200-54759600	Weak transcription	Small Intestine	intestine
22	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:54752400-54757000	Weak transcription	Hela-S3	cervix
25	chr2:54752400-54758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:54752400-54758000	Weak transcription	Aorta	Aorta
27	chr2:54752400-54758000	Weak transcription	NHEK	skin
28	chr2:54752400-54758200	Weak transcription	Fetal Thymus	thymus
29	chr2:54752400-54759600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:54752600-54758000	Weak transcription	HMEC	breast
31	chr2:54752600-54758600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:54752600-54759800	Weak transcription	GM12878-XiMat	blood
33	chr2:54753000-54758800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:54753000-54759000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:54753200-54756200	Strong transcription	HepG2	liver
36	chr2:54753200-54756400	Genic enhancers	HSMMtube	muscle
37	chr2:54753200-54756800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:54753200-54756800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:54753200-54757000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:54753200-54757400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr2:54753200-54757400	Strong transcription	Fetal Brain Female	brain
42	chr2:54753200-54758000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:54753200-54758200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:54753200-54759800	Strong transcription	Adipose Nuclei	Adipose
45	chr2:54753400-54756800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:54753400-54757200	Strong transcription	HUVEC	blood vessel
47	chr2:54753400-54757400	Strong transcription	NHDF-Ad	bronchial
48	chr2:54753400-54757600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:54753400-54758600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:54753400-54758800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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