Variant report

Variant	rs13140802
Chromosome Location	chr4:143323007-143323008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143319256..143323277-chr4:143393099..143396432,4	MCF-7	breast:
2	chr4:143322243..143323903-chr4:143325098..143328296,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11722756	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511267	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128245	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13135641	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138212	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1489577	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1489578	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497389	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565306	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982966	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173209	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306913	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34830426	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35151914	0.87[ASN][1000 genomes]
rs3775703	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775705	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775706	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775710	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775711	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822157	0.88[ASN][1000 genomes]
rs6825345	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72724560	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699598	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs881611	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs983767	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143300200-143326200	Weak transcription	Aorta	Aorta
2	chr4:143301200-143326200	Weak transcription	Gastric	stomach
3	chr4:143301600-143323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:143301600-143325400	Weak transcription	Left Ventricle	heart
5	chr4:143308200-143323200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:143309000-143323200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:143309000-143323400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:143313000-143326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:143316000-143323200	Weak transcription	Small Intestine	intestine
10	chr4:143316400-143323400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:143318000-143323200	Weak transcription	NHLF	lung
12	chr4:143318000-143324000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:143318600-143323200	Weak transcription	NH-A	brain
14	chr4:143318800-143323200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:143320600-143324600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr4:143320600-143326600	Active TSS	Primary T cells fromperipheralblood	blood
17	chr4:143320800-143323600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr4:143320800-143328000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:143321000-143326800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:143321200-143323200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:143321200-143323200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:143321200-143323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:143321200-143323400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:143321400-143323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:143321400-143326600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:143321400-143326600	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr4:143321600-143324400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:143321600-143324400	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr4:143321800-143324200	Transcr. at gene 5' and 3'	HMEC	breast
30	chr4:143322000-143323200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:143322000-143323400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:143322000-143323800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:143322000-143326400	Active TSS	Fetal Muscle Leg	muscle
34	chr4:143322200-143323200	Weak transcription	Fetal Heart	heart
35	chr4:143322200-143323400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr4:143322200-143324400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:143322200-143326600	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr4:143322200-143326600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr4:143322400-143323200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr4:143322400-143323200	Weak transcription	Spleen	Spleen
41	chr4:143322400-143323400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:143322400-143324000	Weak transcription	Psoas Muscle	Psoas
43	chr4:143322400-143324800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:143322400-143326400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:143322600-143323200	Genic enhancers	NHEK	skin
46	chr4:143322600-143323400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:143322600-143325400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:143322600-143326600	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr4:143322800-143323200	Genic enhancers	HSMM	muscle
50	chr4:143322800-143323200	Enhancers	Osteobl	bone

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