Variant report

Variant	rs28519617
Chromosome Location	chr3:135874930-135874931
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135873199..135876113-chr3:135913654..135915671,2	K562	blood:
2	chr3:135871018..135872662-chr3:135874899..135876560,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10222451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512990	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11720497	1.00[ASN][1000 genomes]
rs12330335	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695644	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13068210	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079205	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13081671	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13082532	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321220	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393786	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393787	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535121	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34864445	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35320690	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35352346	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35837273	1.00[ASN][1000 genomes]
rs3905668	0.87[EUR][1000 genomes]
rs56398805	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439629	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67109185	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67589653	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6767060	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769762	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792630	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6793835	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6799056	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6799320	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73222243	0.81[EUR][1000 genomes]
rs9653930	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9826454	0.86[AFR][1000 genomes]
rs9834966	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9848926	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9870122	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9872178	0.83[AFR][1000 genomes]
rs9881400	0.89[AMR][1000 genomes];0.96[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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv877518	chr3:135861666-135885554	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv967232	chr3:135871526-135887926	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv967069	chr3:135874787-135875388	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135845600-135880400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:135862000-135904800	Weak transcription	Hela-S3	cervix
3	chr3:135864200-135882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:135864400-135882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:135864400-135885200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:135865600-135882400	Weak transcription	Fetal Heart	heart
7	chr3:135868800-135883000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:135869000-135876400	Weak transcription	HSMMtube	muscle
9	chr3:135869800-135882400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:135870400-135876000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:135870400-135881000	Weak transcription	Right Atrium	heart
12	chr3:135870800-135895200	Weak transcription	Fetal Intestine Small	intestine
13	chr3:135871000-135881800	Weak transcription	Right Ventricle	heart
14	chr3:135871000-135882400	Weak transcription	Esophagus	oesophagus
15	chr3:135871000-135882400	Weak transcription	Small Intestine	intestine
16	chr3:135871000-135897600	Weak transcription	Aorta	Aorta
17	chr3:135871200-135876000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:135871200-135882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:135871200-135905000	Weak transcription	Fetal Stomach	stomach
20	chr3:135871400-135875200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:135871400-135880000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:135871400-135880200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:135871400-135882200	Weak transcription	HUVEC	blood vessel
24	chr3:135871400-135882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:135871400-135885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:135871400-135885000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:135871400-135885600	Weak transcription	Fetal Kidney	kidney
28	chr3:135871600-135875000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:135871600-135880000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:135871600-135880400	Weak transcription	Adipose Nuclei	Adipose
31	chr3:135871600-135880800	Weak transcription	Psoas Muscle	Psoas
32	chr3:135871600-135881800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:135871600-135882200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:135871600-135882400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:135871600-135882400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:135871600-135882400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:135871600-135883000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:135871600-135884800	Weak transcription	K562	blood
39	chr3:135871600-135885000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:135871800-135876400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:135871800-135877000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr3:135871800-135882200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr3:135872000-135876200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:135872000-135876600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:135872000-135877200	Weak transcription	Primary T cells from cord blood	blood
46	chr3:135872000-135877400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:135872000-135882200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:135872000-135882200	Weak transcription	Primary B cells from cord blood	blood
49	chr3:135872000-135882200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:135872000-135882400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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