Variant report

Variant	rs6739099
Chromosome Location	chr2:54823310-54823311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54823186..54826195-chr2:54832588..54835705,3	K562	blood:
2	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
3	chr2:54822318..54824059-chr2:54829758..54831616,2	MCF-7	breast:
4	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
5	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:
6	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:
7	chr2:54822696..54824811-chr2:54826177..54828033,3	K562	blood:
8	chr2:54816128..54819257-chr2:54823273..54825897,3	MCF-7	breast:
9	chr2:54818034..54820422-chr2:54821780..54823433,2	MCF-7	breast:

No data

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164713	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10165641	0.86[EUR][1000 genomes]
rs1027950	0.82[CEU][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs1052788	0.80[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1052820	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs1112919	0.88[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12463484	0.84[EUR][1000 genomes]
rs12467653	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12473338	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12475342	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12475598	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12476489	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12615589	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622708	0.83[EUR][1000 genomes]
rs13387476	0.88[EUR][1000 genomes]
rs17416284	0.92[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2007020	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3796012	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3817163	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4283459	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519565	0.96[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4557016	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4567979	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671223	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671224	0.96[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4671227	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671229	0.82[CEU][hapmap]
rs4671952	0.92[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4671959	0.95[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671962	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671964	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671965	0.89[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671966	0.86[AFR][1000 genomes]
rs59871921	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60294349	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545428	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6545433	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705756	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6738725	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs67457439	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68134840	0.83[EUR][1000 genomes]
rs72618663	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72618664	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309255	0.92[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv961318	chr2:54818096-54823449	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6739099	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:54815400-54823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:54816800-54823400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:54817000-54825800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:54817000-54826200	Weak transcription	NHDF-Ad	bronchial
10	chr2:54817400-54823400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:54817400-54825400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:54817600-54823600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:54817600-54825000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:54817600-54825600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:54817800-54823400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:54817800-54825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:54817800-54826200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:54817800-54826200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:54818000-54824400	Weak transcription	HMEC	breast
20	chr2:54818000-54826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:54820200-54823600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:54820400-54823400	Enhancers	Primary B cells from cord blood	blood
23	chr2:54820600-54824200	Weak transcription	Fetal Brain Female	brain
24	chr2:54820600-54824600	Weak transcription	Fetal Brain Male	brain
25	chr2:54820800-54823400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:54820800-54823600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:54820800-54826000	Weak transcription	Osteobl	bone
28	chr2:54820800-54826200	Weak transcription	Hela-S3	cervix
29	chr2:54821000-54824400	Weak transcription	NHEK	skin
30	chr2:54821200-54824800	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:54821400-54823400	Genic enhancers	GM12878-XiMat	blood
32	chr2:54821400-54823800	Weak transcription	HSMMtube	muscle
33	chr2:54821800-54823600	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr2:54822000-54823600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr2:54822200-54823600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:54822200-54826200	Enhancers	Brain Cingulate Gyrus	brain
37	chr2:54822200-54827800	Genic enhancers	Fetal Muscle Leg	muscle
38	chr2:54822200-54828800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:54822200-54833800	Genic enhancers	HepG2	liver
40	chr2:54822400-54823400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr2:54822400-54823400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:54822400-54823400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:54822400-54823400	Genic enhancers	Lung	lung
44	chr2:54822400-54823600	Enhancers	Fetal Heart	heart
45	chr2:54822400-54823600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr2:54822400-54823800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:54822400-54824000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:54822400-54824000	Genic enhancers	NHLF	lung
49	chr2:54822400-54824200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:54822400-54825200	Enhancers	Sigmoid Colon	Sigmoid Colon

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