Variant report

Variant	rs899186
Chromosome Location	chr5:16551624-16551625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16489016..16490586-chr5:16549603..16551831,16	MCF-7	breast:
2	chr5:16464191..16467356-chr5:16550758..16555048,4	MCF-7	breast:
3	chr5:16464664..16468967-chr5:16550609..16554281,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173545	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10053236	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1020952	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12109050	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1240647	0.85[ASN][1000 genomes]
rs1551936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162758	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs162862	0.82[AFR][1000 genomes]
rs1991468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991469	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991470	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1991471	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1991472	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2019248	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560829	0.82[ASN][1000 genomes]
rs2560830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560831	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560832	0.84[ASN][1000 genomes]
rs2617422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617423	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617426	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31283	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31288	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334485	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs334486	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs334487	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs334490	0.80[ASN][1000 genomes]
rs334491	0.81[JPT][hapmap]
rs425779	0.81[ASN][1000 genomes]
rs595358	0.80[ASN][1000 genomes]
rs6858960	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs991891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994099	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:16536800-16552800	Weak transcription	Thymus	Thymus
3	chr5:16539200-16554400	Weak transcription	Small Intestine	intestine
4	chr5:16541200-16552000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:16542600-16567200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:16543400-16552800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:16544000-16562400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:16544200-16565200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:16545000-16574600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:16546200-16552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:16546200-16552800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:16546200-16559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:16547400-16552800	Weak transcription	HSMM	muscle
16	chr5:16548600-16552000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:16548800-16552400	Weak transcription	Fetal Intestine Small	intestine
18	chr5:16549200-16554400	Weak transcription	Fetal Intestine Large	intestine
19	chr5:16549200-16569000	Weak transcription	Left Ventricle	heart
20	chr5:16549200-16580200	Weak transcription	Gastric	stomach
21	chr5:16549400-16552200	Weak transcription	Brain Anterior Caudate	brain
22	chr5:16549800-16552000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:16549800-16552200	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:16550000-16551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:16550000-16552200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:16550000-16552400	Strong transcription	Primary T cells from cord blood	blood
27	chr5:16550200-16552000	Weak transcription	Brain Angular Gyrus	brain
28	chr5:16550200-16552200	Weak transcription	Brain Substantia Nigra	brain
29	chr5:16550400-16556800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:16550400-16557400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:16550600-16552400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:16550600-16553200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr5:16550600-16553400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:16550800-16551800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr5:16550800-16551800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:16550800-16554200	Weak transcription	Pancreas	Pancrea
37	chr5:16550800-16555400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr5:16551000-16552800	Weak transcription	Hela-S3	cervix
39	chr5:16551200-16552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:16551200-16553000	Enhancers	NHDF-Ad	bronchial
41	chr5:16551400-16553000	Enhancers	Fetal Muscle Leg	muscle
42	chr5:16551600-16552200	Enhancers	Right Atrium	heart
43	chr5:16551600-16553200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr5:16551600-16553200	Enhancers	Psoas Muscle	Psoas
45	chr5:16551600-16553400	Enhancers	Fetal Heart	heart
46	chr5:16551600-16553400	Enhancers	HSMMtube	muscle

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