Variant report

Variant	rs4567979
Chromosome Location	chr2:54792214-54792215
allele	A/C
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	chr2:54790537..54793498-chr2:54814882..54817196,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10164713	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10165641	0.89[EUR][1000 genomes]
rs1027950	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1052788	0.81[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1052820	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1112919	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs12463484	0.87[EUR][1000 genomes]
rs12467653	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12473338	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12475342	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs12475598	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476489	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615589	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12622708	0.86[EUR][1000 genomes]
rs13387476	0.91[EUR][1000 genomes]
rs17416284	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2007020	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs3796012	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817163	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4283459	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4519565	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4557016	0.88[EUR][1000 genomes]
rs4671223	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4671224	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4671227	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671952	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671959	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671962	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671964	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671965	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs60294349	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545428	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6545433	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545438	0.87[CHB][hapmap]
rs6705756	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs6738725	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs6739099	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67457439	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68134840	0.86[EUR][1000 genomes]
rs72618663	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72618664	0.84[ASN][1000 genomes]
rs9309255	0.92[CEU][hapmap];0.81[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
rs4567979	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54786400-54793200	Enhancers	Fetal Heart	heart
2	chr2:54787600-54796800	Weak transcription	Aorta	Aorta
3	chr2:54787600-54797000	Weak transcription	Gastric	stomach
4	chr2:54787800-54796200	Weak transcription	Esophagus	oesophagus
5	chr2:54787800-54797200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:54788000-54796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:54788200-54795000	Weak transcription	Brain Anterior Caudate	brain
8	chr2:54788400-54797600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:54788600-54795200	Weak transcription	Placenta	Placenta
10	chr2:54788600-54796000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:54788600-54796200	Weak transcription	Colonic Mucosa	Colon
12	chr2:54788600-54796200	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:54788600-54796400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:54788600-54796800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:54788600-54796800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:54788800-54796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:54789200-54796200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:54789400-54792800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:54789400-54795800	Weak transcription	NHLF	lung
20	chr2:54789400-54796000	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:54789400-54796000	Weak transcription	HSMMtube	muscle
22	chr2:54789400-54796200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:54789400-54796200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:54789400-54796400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54789600-54792400	Weak transcription	HUVEC	blood vessel
26	chr2:54789600-54792800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr2:54789600-54795200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:54789600-54795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:54789600-54795800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:54789600-54795800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:54789600-54795800	Weak transcription	NH-A	brain
32	chr2:54789600-54796000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:54789600-54796000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:54789600-54796000	Weak transcription	Brain Substantia Nigra	brain
35	chr2:54789600-54796000	Weak transcription	HMEC	breast
36	chr2:54789600-54796000	Weak transcription	HSMM	muscle
37	chr2:54789600-54796000	Weak transcription	NHDF-Ad	bronchial
38	chr2:54789600-54796000	Weak transcription	Osteobl	bone
39	chr2:54789600-54796200	Enhancers	Primary B cells from peripheral blood	blood
40	chr2:54789600-54796800	Weak transcription	Psoas Muscle	Psoas
41	chr2:54789800-54795000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:54789800-54795200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:54789800-54795800	Weak transcription	NHEK	skin
44	chr2:54789800-54796000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:54789800-54801400	Enhancers	Liver	Liver
46	chr2:54790000-54793200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr2:54790000-54795800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:54790000-54796000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr2:54790000-54796200	Weak transcription	Fetal Brain Male	brain
50	chr2:54790000-54797200	Weak transcription	Lung	lung

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