Variant report

Variant	rs1558149
Chromosome Location	chr5:127293823-127293824
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127290516..127294335-chr5:127417480..127422773,4	MCF-7	breast:
2	chr5:127292969..127298749-chr5:127417448..127421101,7	MCF-7	breast:
3	chr5:127291358..127294527-chr5:127295144..127299558,4	K562	blood:
4	chr5:127263364..127266213-chr5:127293562..127295793,3	MCF-7	breast:
5	chr5:127293751..127296384-chr5:127304334..127306609,2	MCF-7	breast:
6	chr5:127211016..127213453-chr5:127292897..127295874,2	MCF-7	breast:
7	chr5:127293327..127295485-chr5:127298267..127301058,2	MCF-7	breast:
8	chr5:127293170..127295868-chr5:127299899..127303794,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10040931	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10041355	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10041388	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10052149	0.85[EUR][1000 genomes]
rs10055964	0.92[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10057048	0.85[EUR][1000 genomes]
rs10059403	0.89[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs10076010	0.84[EUR][1000 genomes]
rs1013374	0.92[EUR][1000 genomes]
rs1013375	0.92[EUR][1000 genomes]
rs10463836	0.80[EUR][1000 genomes]
rs10478786	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10478787	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10478788	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10478790	0.84[EUR][1000 genomes]
rs10478792	0.88[CEU][hapmap]
rs10519968	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10519977	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs11745009	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11745023	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs12523625	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13154863	0.82[EUR][1000 genomes]
rs13161109	0.82[EUR][1000 genomes]
rs13174053	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13177354	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs13180050	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13184942	0.80[EUR][1000 genomes]
rs17606751	0.89[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2041143	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2108652	0.85[EUR][1000 genomes]
rs2108654	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2159110	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2409038	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2409039	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2409040	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2898077	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34498802	0.82[EUR][1000 genomes]
rs35713319	0.84[EUR][1000 genomes]
rs4835934	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4836352	0.81[EUR][1000 genomes]
rs5008451	0.88[CEU][hapmap]
rs59634534	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6867103	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs6867442	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6867465	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6867644	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6881456	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6889393	0.85[EUR][1000 genomes]
rs6892704	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6897353	0.81[EUR][1000 genomes]
rs732235	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs732236	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs768528	0.93[EUR][1000 genomes]
rs7711776	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs7713606	0.92[EUR][1000 genomes]
rs7717705	0.92[EUR][1000 genomes]
rs7722601	0.83[ASN][1000 genomes]
rs7732912	0.82[EUR][1000 genomes]
rs9327458	0.85[JPT][hapmap]
rs9327460	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs9327461	0.84[EUR][1000 genomes]
rs9327462	0.85[CEU][hapmap];0.89[TSI][hapmap]

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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558149	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:127274800-127295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
4	chr5:127278400-127294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle
6	chr5:127281800-127295400	Weak transcription	Psoas Muscle	Psoas
7	chr5:127285200-127295200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:127286600-127295200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:127287400-127297200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:127288200-127295200	Weak transcription	Primary T cells from cord blood	blood
12	chr5:127289000-127294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:127290400-127294600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
15	chr5:127290800-127295400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:127290800-127297400	Weak transcription	Spleen	Spleen
17	chr5:127291600-127295000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:127292200-127294600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr5:127292200-127297600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr5:127292400-127296400	Enhancers	Left Ventricle	heart
21	chr5:127292600-127296400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr5:127292600-127296400	Enhancers	HepG2	liver
23	chr5:127292600-127298400	Enhancers	Fetal Intestine Large	intestine
24	chr5:127292600-127298600	Enhancers	Fetal Intestine Small	intestine
25	chr5:127292800-127294000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr5:127292800-127294800	Enhancers	Brain Cingulate Gyrus	brain
27	chr5:127292800-127295000	Enhancers	Colon Smooth Muscle	Colon
28	chr5:127292800-127295200	Enhancers	Fetal Brain Female	brain
29	chr5:127292800-127295600	Enhancers	Brain Anterior Caudate	brain
30	chr5:127292800-127296200	Enhancers	Brain Substantia Nigra	brain
31	chr5:127292800-127296400	Enhancers	Brain Hippocampus Middle	brain
32	chr5:127292800-127297200	Enhancers	Fetal Lung	lung
33	chr5:127292800-127297600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr5:127292800-127297800	Enhancers	HUVEC	blood vessel
35	chr5:127292800-127298400	Enhancers	Fetal Heart	heart
36	chr5:127292800-127314400	Weak transcription	Pancreas	Pancrea
37	chr5:127293000-127294000	Enhancers	Colonic Mucosa	Colon
38	chr5:127293000-127294400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:127293000-127294600	Enhancers	Duodenum Mucosa	Duodenum
40	chr5:127293000-127295200	Weak transcription	Osteobl	bone
41	chr5:127293000-127295600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:127293000-127295800	Flanking Active TSS	A549	lung
43	chr5:127293000-127297600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr5:127293000-127298600	Enhancers	Stomach Mucosa	stomach
45	chr5:127293200-127294200	Weak transcription	Adipose Nuclei	Adipose
46	chr5:127293200-127295000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:127293200-127295000	Weak transcription	NHLF	lung
48	chr5:127293200-127295400	Weak transcription	HSMM	muscle
49	chr5:127293200-127297400	Weak transcription	Gastric	stomach
50	chr5:127293200-127301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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