Variant report

Variant	rs2529390
Chromosome Location	chr7:50701355-50701356
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	chr7:50535443..50536367-chr7:50700303..50701436,9	MCF-7	breast:
2	chr7:50699706..50701584-chr7:50708525..50710076,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2108348	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108352	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108353	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2158919	0.94[AFR][1000 genomes]
rs2190495	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237443	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237444	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237445	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237446	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237459	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245966	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262464	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2262465	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329487	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329488	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429073	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465529	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529383	0.92[AFR][1000 genomes]
rs2529384	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529385	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529386	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529387	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529388	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529389	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529391	0.93[AFR][1000 genomes]
rs2529427	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529428	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715112	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2715113	0.89[AFR][1000 genomes]
rs2715114	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715116	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4513921	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947757	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6948032	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6970413	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50674200-50709800	Weak transcription	Esophagus	oesophagus
2	chr7:50682600-50704600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:50693600-50705400	Weak transcription	NH-A	brain
4	chr7:50694200-50729200	Weak transcription	Hela-S3	cervix
5	chr7:50694600-50707800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:50694600-50708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:50695000-50720600	Weak transcription	Primary T cells from cord blood	blood
8	chr7:50695600-50716000	Weak transcription	Fetal Stomach	stomach
9	chr7:50697600-50716600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:50697800-50716800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:50698200-50708800	Weak transcription	HSMMtube	muscle
12	chr7:50699600-50702200	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:50699600-50707800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:50699600-50720400	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:50700600-50707800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:50700600-50709000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:50700600-50709200	Weak transcription	Gastric	stomach
18	chr7:50700600-50709400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:50700600-50722000	Weak transcription	Aorta	Aorta
20	chr7:50700800-50701400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr7:50700800-50701400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:50700800-50702200	Weak transcription	Psoas Muscle	Psoas
23	chr7:50700800-50705000	Weak transcription	HepG2	liver
24	chr7:50700800-50705600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:50700800-50707600	Weak transcription	Brain Substantia Nigra	brain
26	chr7:50700800-50707800	Weak transcription	Right Atrium	heart
27	chr7:50700800-50708400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:50700800-50709000	Weak transcription	Lung	lung
29	chr7:50700800-50709200	Weak transcription	Adipose Nuclei	Adipose
30	chr7:50701000-50702000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:50701000-50702200	Weak transcription	Small Intestine	intestine
32	chr7:50701000-50702600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:50701000-50708000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:50701000-50708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:50701000-50708000	Weak transcription	Pancreas	Pancrea
36	chr7:50701000-50708200	Weak transcription	Brain Anterior Caudate	brain
37	chr7:50701000-50709200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:50701000-50709600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr7:50701000-50712400	Weak transcription	Ovary	ovary
40	chr7:50701000-50719400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:50701000-50720400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:50701000-50733600	Weak transcription	A549	lung
43	chr7:50701200-50703800	Weak transcription	HUVEC	blood vessel
44	chr7:50701200-50705200	Weak transcription	Liver	Liver
45	chr7:50701200-50705400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:50701200-50706200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr7:50701200-50708400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:50701200-50717800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:50701200-50728800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:50701200-50731200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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