Variant report

Variant	rs2269874
Chromosome Location	chr4:7780927-7780928
allele	G/T
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	chr4:7780788-7781407	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr4:7780425-7781361	PANC-1	pancreas:	n/a	n/a
3	REST	chr4:7780455-7781510	H1-neurons	neurons:	n/a	n/a
4	REST	chr4:7780739-7781321	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr4:7775971-7782690	K562	blood:	n/a	n/a
6	IRF1	chr4:7780432-7781117	K562	blood:	n/a	chr4:7780729-7780750
7	POLR2A	chr4:7780727-7780972	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr4:7780725-7781369	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10440168	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733791	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11933506	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11938080	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119259	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13127069	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13128692	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2269852	0.86[CHB][hapmap]
rs4274845	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4689864	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4689868	1.00[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446623	0.82[CEU][hapmap]
rs6839744	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9683795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
10	chr4:7766800-7781200	Strong transcription	HUVEC	blood vessel
11	chr4:7767600-7781000	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:7772000-7783000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:7773600-7782800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:7773600-7783000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:7773600-7783600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:7773800-7783400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:7774000-7782800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:7774000-7783400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:7774200-7781600	Strong transcription	A549	lung
21	chr4:7774400-7781000	Weak transcription	Fetal Heart	heart
22	chr4:7774600-7783000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:7774600-7783400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:7775200-7782400	Strong transcription	Placenta	Placenta
25	chr4:7775400-7783400	Weak transcription	Small Intestine	intestine
26	chr4:7776000-7784400	Strong transcription	Fetal Intestine Small	intestine
27	chr4:7776200-7781000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:7776400-7787200	Weak transcription	Fetal Brain Male	brain
29	chr4:7776400-7790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:7776600-7783000	Weak transcription	Right Ventricle	heart
34	chr4:7776600-7783200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:7776600-7785400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:7777000-7783600	Strong transcription	HMEC	breast
37	chr4:7777000-7785800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:7777200-7783400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:7777400-7784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:7778000-7781600	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr4:7778000-7783000	Weak transcription	Left Ventricle	heart
42	chr4:7778000-7784400	Strong transcription	Fetal Brain Female	brain
43	chr4:7778200-7781400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:7778800-7781000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:7779000-7781000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:7779000-7781000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:7779000-7781200	Genic enhancers	Colonic Mucosa	Colon
48	chr4:7779000-7781400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
49	chr4:7779200-7781000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:7779200-7781000	Strong transcription	Esophagus	oesophagus

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