Variant report

Variant	rs28638437
Chromosome Location	chr7:40045020-40045021
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39987570..39989729-chr7:40044473..40047444,2	MCF-7	breast:
2	chr7:39988360..39989993-chr7:40043124..40045978,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259826	Chromatin interaction
ENSG00000065883	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10046564	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10224206	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10225492	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235989	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239324	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247292	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253590	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272514	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277853	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10279016	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082023	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12701787	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231977	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239106	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241453	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310449	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310480	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17435812	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496226	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496247	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526699	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140254	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329611	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492942	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547436	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326687	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470312	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748607	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35052806	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35082351	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35618050	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273753	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4428576	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481477	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498451	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947071	0.81[EUR][1000 genomes]
rs73127832	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127862	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773382	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780996	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809558	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs878785	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9639817	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9639820	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9655407	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690347	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9986996	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986997	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv464436	chr7:40018693-40133044	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv606706	chr7:40018693-40133044	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv606707	chr7:40021044-40133044	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv606708	chr7:40021044-40157040	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv887978	chr7:40030488-40124137	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:40018600-40047800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:40020400-40077600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:40023400-40046800	Weak transcription	HMEC	breast
5	chr7:40025600-40046800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:40025600-40055400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:40025800-40054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:40025800-40055400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:40025800-40055400	Weak transcription	Fetal Heart	heart
10	chr7:40025800-40055400	Weak transcription	Stomach Mucosa	stomach
11	chr7:40025800-40059600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:40025800-40062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:40025800-40082200	Weak transcription	Spleen	Spleen
14	chr7:40026000-40071200	Weak transcription	Brain Germinal Matrix	brain
15	chr7:40026600-40096800	Weak transcription	Right Ventricle	heart
16	chr7:40027400-40045400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:40027800-40047400	Weak transcription	Fetal Kidney	kidney
18	chr7:40027800-40047600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:40027800-40047800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:40027800-40048400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:40027800-40049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:40027800-40053800	Weak transcription	HepG2	liver
23	chr7:40027800-40054800	Weak transcription	Aorta	Aorta
24	chr7:40027800-40055400	Weak transcription	Fetal Brain Female	brain
25	chr7:40028000-40047400	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:40028000-40047400	Weak transcription	HSMMtube	muscle
27	chr7:40028000-40047800	Weak transcription	NH-A	brain
28	chr7:40028000-40077800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr7:40028000-40127800	Weak transcription	Colonic Mucosa	Colon
30	chr7:40028200-40047400	Weak transcription	Hela-S3	cervix
31	chr7:40028200-40047800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:40028200-40048000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:40028200-40073000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr7:40028600-40049400	Weak transcription	Thymus	Thymus
35	chr7:40032200-40049400	Weak transcription	Lung	lung
36	chr7:40032200-40049600	Weak transcription	Fetal Stomach	stomach
37	chr7:40032200-40049800	Weak transcription	Ovary	ovary
38	chr7:40032800-40047600	Weak transcription	Brain Anterior Caudate	brain
39	chr7:40033200-40047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:40033600-40047600	Weak transcription	Brain Angular Gyrus	brain
41	chr7:40034400-40072200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr7:40036600-40053000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:40037000-40046000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr7:40038800-40050000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr7:40039200-40045200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr7:40039400-40046200	Strong transcription	Fetal Thymus	thymus
47	chr7:40039600-40047800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr7:40040000-40047800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:40040200-40045400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:40040400-40045600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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