Variant report

Variant	rs4671223
Chromosome Location	chr2:54741325-54741326
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	chr2:54739309..54741349-chr2:54741528..54743600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10165641	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1052820	0.88[CEU][hapmap]
rs1112919	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12463484	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12467653	0.81[EUR][1000 genomes]
rs12475598	0.82[EUR][1000 genomes]
rs12476489	0.80[EUR][1000 genomes]
rs12477376	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12622708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13387476	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17045941	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17416284	0.88[CEU][hapmap]
rs3817163	0.88[CEU][hapmap]
rs4283459	0.84[EUR][1000 genomes]
rs4519565	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs4567979	0.87[EUR][1000 genomes]
rs4671224	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671227	0.87[EUR][1000 genomes]
rs4671952	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs4671959	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4671962	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671965	0.92[CEU][hapmap]
rs60294349	0.82[EUR][1000 genomes]
rs6545428	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs6545433	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6705756	0.85[CEU][hapmap]
rs6717713	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6717816	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6738725	0.80[CEU][hapmap]
rs6739099	0.84[EUR][1000 genomes]
rs68134840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9309255	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[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
rs4671223	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
5	chr2:54733600-54747000	Weak transcription	Gastric	stomach
6	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
8	chr2:54737600-54743200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
10	chr2:54738200-54743200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:54738200-54743800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:54738200-54746400	Weak transcription	NHLF	lung
14	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
15	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:54738400-54743200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:54738400-54743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:54738400-54746200	Weak transcription	A549	lung
19	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:54739000-54742400	Enhancers	Fetal Lung	lung
21	chr2:54739200-54742600	Enhancers	Fetal Heart	heart
22	chr2:54739400-54746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:54740000-54742600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:54740200-54743800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:54740400-54741600	Weak transcription	Left Ventricle	heart
26	chr2:54740400-54741800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:54740400-54742000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:54740400-54742000	Weak transcription	Ovary	ovary
29	chr2:54740400-54742200	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:54740400-54743800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:54740400-54743800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:54740400-54743800	Weak transcription	Spleen	Spleen
33	chr2:54740400-54744200	Weak transcription	Lung	lung
34	chr2:54740400-54746200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:54740400-54746200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:54740400-54746200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:54740400-54746200	Weak transcription	Right Atrium	heart
38	chr2:54740400-54746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:54740400-54746400	Weak transcription	Psoas Muscle	Psoas
40	chr2:54740400-54747000	Weak transcription	Pancreas	Pancrea
41	chr2:54740400-54747800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:54740400-54751600	Weak transcription	Placenta	Placenta
43	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
44	chr2:54740600-54742000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:54740600-54742000	Weak transcription	Right Ventricle	heart
46	chr2:54740600-54743200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:54740600-54743200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:54740600-54743600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:54740600-54745200	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:54740600-54746200	Weak transcription	NHDF-Ad	bronchial

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