Variant report

Variant	rs3936645
Chromosome Location	chr4:129304053-129304054
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	chr4:129286542..129289517-chr4:129302527..129305872,3	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11098960	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12643763	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995771	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995772	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3936645	RP11-420A23.1	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129292800-129306600	Weak transcription	Psoas Muscle	Psoas
2	chr4:129298600-129304600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:129298600-129305200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:129298600-129305800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:129298600-129307400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:129298800-129305000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:129298800-129307400	Weak transcription	Fetal Intestine Small	intestine
8	chr4:129299000-129307400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:129299800-129305000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:129300000-129306400	Weak transcription	Aorta	Aorta
11	chr4:129301000-129305200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:129301400-129305200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:129301400-129305400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:129301600-129305000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:129301600-129305200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:129301600-129306400	Weak transcription	Hela-S3	cervix
17	chr4:129301800-129304600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:129301800-129305000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:129301800-129306400	Weak transcription	Adipose Nuclei	Adipose
20	chr4:129301800-129306400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:129301800-129314000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:129302000-129304600	Weak transcription	HSMM	muscle
23	chr4:129302000-129305000	Weak transcription	Small Intestine	intestine
24	chr4:129302000-129305200	Weak transcription	Esophagus	oesophagus
25	chr4:129302000-129305200	Weak transcription	A549	lung
26	chr4:129302000-129306200	Weak transcription	Stomach Mucosa	stomach
27	chr4:129302000-129306400	Weak transcription	HMEC	breast
28	chr4:129302200-129304600	Weak transcription	HSMMtube	muscle
29	chr4:129302200-129305200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:129302400-129305200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:129302600-129305200	Weak transcription	Fetal Heart	heart
32	chr4:129303800-129304200	Weak transcription	Placenta	Placenta
33	chr4:129303800-129306400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr4:129303800-129306400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:129304000-129306400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:129304000-129306400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:129304000-129306600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:129304000-129306600	Weak transcription	NHEK	skin

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