Variant report

Variant	rs1219269
Chromosome Location	chr4:143095271-143095272
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143092506..143095371-chr4:143126612..143129573,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1219266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1219268	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1219270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1219271	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1219272	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1219273	0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1219274	0.88[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1219275	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12500144	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1390994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1532450	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs182862	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907113	1.00[CEU][hapmap]
rs1907119	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs1907120	0.83[JPT][hapmap]
rs1907134	0.85[CHD][hapmap]
rs1907135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907137	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1948323	1.00[CEU][hapmap]
rs1994217	0.83[JPT][hapmap]
rs2130685	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs2130687	0.81[JPT][hapmap]
rs2172023	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs2200997	0.80[CHD][hapmap]
rs2247587	0.85[CHD][hapmap]
rs2627798	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2627801	0.93[CHD][hapmap];0.87[JPT][hapmap]
rs2627804	0.82[CHD][hapmap]
rs2627813	0.85[CHD][hapmap]
rs2627817	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs2627834	0.80[EUR][1000 genomes]
rs2627835	0.87[CEU][hapmap]
rs2636632	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs2636637	0.81[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2636643	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs2636655	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2636656	1.00[CEU][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs2636657	0.80[EUR][1000 genomes]
rs2636660	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs2636666	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2636679	1.00[CEU][hapmap]
rs2636682	0.82[JPT][hapmap]
rs2636683	0.83[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2636686	0.85[CHD][hapmap]
rs2645808	0.90[AFR][1000 genomes]
rs3102438	1.00[CEU][hapmap]
rs3102439	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs3113511	1.00[CEU][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs3113521	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3113522	0.87[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs336384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336388	0.84[ASN][1000 genomes]
rs336393	0.85[TSI][hapmap]
rs336394	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs336400	0.81[CEU][hapmap]
rs336402	0.81[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs336405	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs336406	0.81[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs336408	0.81[JPT][hapmap];0.84[TSI][hapmap]
rs34648309	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs992257	0.81[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv595604	chr4:143077401-143228914	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:143049800-143114400	Weak transcription	Right Ventricle	heart
3	chr4:143052400-143111600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:143057800-143114400	Weak transcription	Aorta	Aorta
5	chr4:143058000-143181000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:143061800-143102200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:143069800-143112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:143070400-143134400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:143071000-143117800	Weak transcription	Psoas Muscle	Psoas
10	chr4:143072000-143137000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:143076800-143107200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:143076800-143113200	Weak transcription	Pancreas	Pancrea
13	chr4:143078200-143103400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:143081000-143128200	Weak transcription	NHDF-Ad	bronchial
15	chr4:143082000-143130000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:143082400-143134800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:143082800-143115800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:143083200-143100000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:143084600-143099600	Weak transcription	Fetal Heart	heart
20	chr4:143086800-143096600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:143088600-143108200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:143088800-143096200	Weak transcription	Ovary	ovary
23	chr4:143089000-143096400	Strong transcription	HMEC	breast
24	chr4:143089000-143108400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:143089400-143118000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:143089800-143095800	Strong transcription	Dnd41	blood
27	chr4:143089800-143100000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:143090000-143117400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:143090200-143096200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:143091400-143097200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:143091600-143095600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:143091600-143096400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:143091600-143096400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:143091600-143100600	Strong transcription	HSMMtube	muscle
35	chr4:143091600-143106200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:143092000-143103200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:143092400-143116200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:143092400-143131000	Weak transcription	Fetal Intestine Large	intestine
39	chr4:143093000-143104200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:143094000-143098800	Strong transcription	Primary T cells from cord blood	blood
41	chr4:143094200-143096000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:143094200-143096400	Strong transcription	NHEK	skin
43	chr4:143094200-143105400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:143094800-143114000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:143095000-143095400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr4:143095000-143096800	Weak transcription	Osteobl	bone
47	chr4:143095000-143097000	Weak transcription	HSMM	muscle
48	chr4:143095000-143097800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:143095000-143102000	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:143095000-143115400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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