Variant report

Variant	rs1497393
Chromosome Location	chr4:143273711-143273712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143272659..143276206-chr4:143392332..143397078,7	MCF-7	breast:
2	chr4:143272607..143274373-chr4:143277065..143279303,2	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:23)

rs_ID	r²[population]
rs10021260	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10428305	0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1120454	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723890	0.89[GIH][hapmap]
rs12499068	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs12640900	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1353624	0.84[GIH][hapmap]
rs1391092	1.00[CEU][hapmap]
rs1497396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565307	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17016001	0.86[GIH][hapmap]
rs17658809	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs2200841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28435783	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28707318	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6827918	0.86[GIH][hapmap]
rs6842192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7666932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9308149	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931420	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998814	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998945	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143258000-143274800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:143258200-143274000	Weak transcription	Dnd41	blood
3	chr4:143264000-143275400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr4:143264600-143274400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:143265800-143280600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr4:143268400-143283200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:143268600-143273800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:143268600-143274000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr4:143268600-143274000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:143269400-143278600	Enhancers	Fetal Heart	heart
11	chr4:143270000-143274200	Weak transcription	NHEK	skin
12	chr4:143270000-143274600	Weak transcription	Ovary	ovary
13	chr4:143270200-143274200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:143270200-143274400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:143270200-143275200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:143270200-143275200	Weak transcription	Psoas Muscle	Psoas
17	chr4:143270200-143275800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:143270400-143274600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:143270600-143274000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:143270800-143284000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:143271000-143277200	Enhancers	Fetal Lung	lung
22	chr4:143271200-143275600	Enhancers	HSMMtube	muscle
23	chr4:143271200-143276800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:143271800-143275400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:143272000-143277000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr4:143272200-143274000	Enhancers	HMEC	breast
27	chr4:143272400-143273800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:143272400-143274000	Weak transcription	Primary T cells from cord blood	blood
29	chr4:143272400-143274000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:143272400-143274000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:143272400-143274000	Weak transcription	Osteobl	bone
32	chr4:143272400-143274200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:143272400-143274600	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:143272400-143275800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:143272400-143276000	Weak transcription	Adipose Nuclei	Adipose
36	chr4:143272400-143278200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:143272400-143279800	Weak transcription	Right Ventricle	heart
38	chr4:143272600-143273800	Weak transcription	Brain Angular Gyrus	brain
39	chr4:143272600-143274000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:143272600-143274000	Weak transcription	Fetal Intestine Large	intestine
41	chr4:143272600-143274000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:143272600-143274400	Weak transcription	Stomach Mucosa	stomach
43	chr4:143272600-143276000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:143272600-143276200	Weak transcription	Small Intestine	intestine
45	chr4:143272800-143273800	Weak transcription	Colon Smooth Muscle	Colon
46	chr4:143272800-143273800	Weak transcription	A549	lung
47	chr4:143272800-143274200	Weak transcription	Fetal Stomach	stomach
48	chr4:143272800-143274400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:143273000-143273800	Active TSS	Stomach Smooth Muscle	stomach
50	chr4:143273000-143274200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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