Variant report

Variant	rs1013375
Chromosome Location	chr5:127277217-127277218
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127269084..127270706-chr5:127275651..127278152,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC12A2-1	chr5:127276874-127277326	ENSG00000230561

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10040931	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10041355	0.94[EUR][1000 genomes]
rs10041388	0.94[EUR][1000 genomes]
rs10055964	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs10059403	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs1013374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478786	0.92[EUR][1000 genomes]
rs10478787	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10478788	0.89[CEU][hapmap]
rs10478792	0.85[CEU][hapmap]
rs10519968	0.82[CEU][hapmap]
rs10519977	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs11745009	0.90[EUR][1000 genomes]
rs11745023	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12523625	0.96[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs13161109	0.83[EUR][1000 genomes]
rs13174053	0.92[EUR][1000 genomes]
rs13177354	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs13180050	0.92[EUR][1000 genomes]
rs1558149	0.96[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs17606751	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs2041143	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2108654	0.92[EUR][1000 genomes]
rs2159110	0.86[EUR][1000 genomes]
rs2409038	0.92[EUR][1000 genomes]
rs2409039	0.91[EUR][1000 genomes]
rs2409040	0.88[EUR][1000 genomes]
rs2898077	0.92[EUR][1000 genomes]
rs4835934	0.92[EUR][1000 genomes]
rs5008451	0.92[CEU][hapmap]
rs59634534	0.92[EUR][1000 genomes]
rs6867103	0.82[CEU][hapmap]
rs6867442	0.89[CEU][hapmap]
rs6867465	0.88[CEU][hapmap]
rs6867644	0.88[CEU][hapmap]
rs6881456	0.93[EUR][1000 genomes]
rs6892704	0.96[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs732235	0.92[EUR][1000 genomes]
rs732236	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs768528	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711776	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs7713606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7717705	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7717741	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs9327458	0.81[CEU][hapmap]
rs9327460	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs9327462	0.82[CEU][hapmap];0.83[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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127267400-127292200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:127269800-127292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:127272400-127277400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:127272600-127277800	Weak transcription	NHEK	skin
6	chr5:127272800-127277800	Weak transcription	GM12878-XiMat	blood
7	chr5:127274400-127287000	Weak transcription	Primary T cells from cord blood	blood
8	chr5:127274800-127295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
10	chr5:127276400-127278000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr5:127276600-127277400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:127276600-127277400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:127276600-127278000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
14	chr5:127276600-127278200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:127276600-127278200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:127276600-127278200	Enhancers	Fetal Stomach	stomach
17	chr5:127276600-127278400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:127276600-127278400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr5:127276600-127278600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:127276600-127279200	Enhancers	Small Intestine	intestine
21	chr5:127276600-127281800	Enhancers	A549	lung
22	chr5:127276800-127277600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:127276800-127277600	Flanking Active TSS	Ovary	ovary
24	chr5:127276800-127277800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr5:127276800-127277800	Enhancers	Fetal Muscle Leg	muscle
26	chr5:127276800-127278000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:127276800-127278000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:127276800-127278000	Enhancers	HepG2	liver
29	chr5:127276800-127278200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:127276800-127278400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:127276800-127278400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:127276800-127278400	Enhancers	Fetal Intestine Large	intestine
33	chr5:127276800-127278600	Enhancers	Fetal Intestine Small	intestine
34	chr5:127276800-127278600	Enhancers	NHDF-Ad	bronchial
35	chr5:127276800-127278600	Enhancers	NHLF	lung
36	chr5:127277000-127277400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:127277000-127277400	Enhancers	Fetal Muscle Trunk	muscle
38	chr5:127277000-127277800	Active TSS	Brain Cingulate Gyrus	brain
39	chr5:127277000-127278200	Enhancers	Fetal Brain Male	brain
40	chr5:127277000-127278400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:127277000-127278600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr5:127277000-127279400	Enhancers	Stomach Mucosa	stomach
43	chr5:127277200-127277400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:127277200-127277400	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr5:127277200-127277400	Enhancers	Brain Germinal Matrix	brain
46	chr5:127277200-127277400	Active TSS	Duodenum Mucosa	Duodenum
47	chr5:127277200-127277400	Enhancers	NH-A	brain
48	chr5:127277200-127277600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr5:127277200-127277600	Active TSS	Brain Anterior Caudate	brain
50	chr5:127277200-127277600	Active TSS	Brain Hippocampus Middle	brain

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