Variant report

Variant	rs10025154
Chromosome Location	chr4:7781560-7781561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:7775971-7782690	K562	blood:	n/a	n/a
2	POLR2A	chr4:7781511-7782123	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10015031	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032821	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12644614	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645231	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1557817	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16841211	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841229	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018399	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107182	0.82[ASN][1000 genomes]
rs28460880	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729246	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234829	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4689161	0.80[ASN][1000 genomes]
rs55689818	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60422709	0.88[EUR][1000 genomes]
rs6446619	0.86[ASN][1000 genomes]
rs6827395	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6828807	0.86[ASN][1000 genomes]
rs6829473	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9790401	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9917925	0.93[AMR][1000 genomes];0.95[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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
3	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
4	chr4:7760000-7783000	Strong transcription	HSMMtube	muscle
5	chr4:7760000-7783200	Strong transcription	HSMM	muscle
6	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
9	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:7772000-7783000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:7773600-7782800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:7773600-7783000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:7773600-7783600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:7773800-7783400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:7774000-7782800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:7774000-7783400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:7774200-7781600	Strong transcription	A549	lung
18	chr4:7774600-7783000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:7774600-7783400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:7775200-7782400	Strong transcription	Placenta	Placenta
21	chr4:7775400-7783400	Weak transcription	Small Intestine	intestine
22	chr4:7776000-7784400	Strong transcription	Fetal Intestine Small	intestine
23	chr4:7776400-7787200	Weak transcription	Fetal Brain Male	brain
24	chr4:7776400-7790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:7776600-7783000	Weak transcription	Right Ventricle	heart
29	chr4:7776600-7783200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:7776600-7785400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:7777000-7783600	Strong transcription	HMEC	breast
32	chr4:7777000-7785800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:7777200-7783400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:7777400-7784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:7778000-7781600	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr4:7778000-7783000	Weak transcription	Left Ventricle	heart
37	chr4:7778000-7784400	Strong transcription	Fetal Brain Female	brain
38	chr4:7779200-7783600	Strong transcription	Brain Germinal Matrix	brain
39	chr4:7779400-7783200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:7779800-7782800	Weak transcription	Primary T cells from cord blood	blood
41	chr4:7779800-7782800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:7780200-7783400	Weak transcription	Aorta	Aorta
43	chr4:7780200-7794400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:7780400-7781600	Weak transcription	Spleen	Spleen
45	chr4:7780400-7781800	Enhancers	Duodenum Mucosa	Duodenum
46	chr4:7780400-7782000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:7780400-7782000	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr4:7780400-7782200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr4:7780400-7782400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:7780400-7784200	Genic enhancers	Fetal Muscle Leg	muscle

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