Variant report

Variant	rs4671227
Chromosome Location	chr2:54790598-54790599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54790164..54792599-chr2:54886849..54889331,2	K562	blood:
2	chr2:54789686..54792599-chr2:54886831..54888349,2	K562	blood:
3	chr2:54789909..54791873-chr2:54794483..54796038,2	MCF-7	breast:
4	chr2:54789266..54791330-chr2:54815899..54818560,2	K562	blood:
5	chr2:54790537..54793498-chr2:54814882..54817196,2	MCF-7	breast:
6	chr2:54789199..54791941-chr2:54810651..54814148,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10164713	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10165641	0.89[EUR][1000 genomes]
rs1052788	0.81[EUR][1000 genomes]
rs1112919	0.89[EUR][1000 genomes]
rs12463484	0.87[EUR][1000 genomes]
rs12467653	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12473338	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12475342	0.86[EUR][1000 genomes]
rs12475598	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12476489	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615589	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12622708	0.85[EUR][1000 genomes]
rs13387476	0.90[EUR][1000 genomes]
rs3796012	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817163	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4283459	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4519565	0.87[EUR][1000 genomes]
rs4557016	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4567979	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671223	0.87[EUR][1000 genomes]
rs4671224	0.89[EUR][1000 genomes]
rs4671952	0.85[EUR][1000 genomes]
rs4671959	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671962	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671964	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671965	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59871921	0.81[ASN][1000 genomes]
rs60294349	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545428	0.87[EUR][1000 genomes]
rs6545433	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739099	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67457439	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68134840	0.87[EUR][1000 genomes]
rs72618663	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72618664	0.87[ASN][1000 genomes]
rs9309255	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671227	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54786400-54793200	Enhancers	Fetal Heart	heart
2	chr2:54787600-54791400	Enhancers	Left Ventricle	heart
3	chr2:54787600-54791400	Weak transcription	Right Ventricle	heart
4	chr2:54787600-54791400	Weak transcription	Spleen	Spleen
5	chr2:54787600-54796800	Weak transcription	Aorta	Aorta
6	chr2:54787600-54797000	Weak transcription	Gastric	stomach
7	chr2:54787800-54790600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:54787800-54796200	Weak transcription	Esophagus	oesophagus
9	chr2:54787800-54797200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:54788000-54791000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:54788000-54791200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:54788000-54796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:54788200-54790600	Enhancers	Fetal Lung	lung
14	chr2:54788200-54795000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:54788400-54790600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:54788400-54790600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr2:54788400-54791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:54788400-54797600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54788600-54790600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:54788600-54791000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:54788600-54791200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:54788600-54791600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:54788600-54791600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:54788600-54791800	Enhancers	Stomach Mucosa	stomach
25	chr2:54788600-54792000	Enhancers	Fetal Thymus	thymus
26	chr2:54788600-54795200	Weak transcription	Placenta	Placenta
27	chr2:54788600-54796000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:54788600-54796200	Weak transcription	Colonic Mucosa	Colon
29	chr2:54788600-54796200	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:54788600-54796400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:54788600-54796800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:54788600-54796800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:54788800-54790600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:54788800-54790600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr2:54788800-54790600	Enhancers	Dnd41	blood
36	chr2:54788800-54791200	Weak transcription	Fetal Kidney	kidney
37	chr2:54788800-54796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:54789000-54790600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:54789000-54790600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr2:54789000-54790600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr2:54789000-54790600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr2:54789000-54790800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr2:54789200-54790600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:54789200-54790800	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:54789200-54796200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:54789400-54790600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:54789400-54791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:54789400-54791800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:54789400-54792000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:54789400-54792800	Weak transcription	Brain Cingulate Gyrus	brain

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