Variant report

Variant	rs12640727
Chromosome Location	chr4:186691074-186691075
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10000785	0.85[AFR][1000 genomes]
rs10027307	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10027404	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12640785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649620	0.90[AFR][1000 genomes]
rs12649994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105380	0.85[AFR][1000 genomes]
rs13112453	0.80[AFR][1000 genomes]
rs28386838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28521093	0.83[AMR][1000 genomes]
rs28526455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28563791	0.85[AFR][1000 genomes]
rs28575175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28682410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28694150	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28696141	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62334849	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62334851	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62334852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62334854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62334855	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62334857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857307	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72703826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654366	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7655720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432684	chr4:186412851-186742851	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020731	chr4:186512433-186724031	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv830171	chr4:186610113-186789271	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1023412	chr4:186613289-186707428	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv537421	chr4:186613289-186707428	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv427702	chr4:186618031-186782377	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
11	nsv1015931	chr4:186683165-186734480	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186655200-186701400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:186661400-186694600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:186664800-186693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:186667600-186691400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:186673000-186714000	Weak transcription	Ovary	ovary
6	chr4:186676600-186694000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:186680600-186702600	Weak transcription	Gastric	stomach
8	chr4:186683400-186692400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:186683400-186694000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:186683400-186694600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:186683400-186695400	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:186683400-186695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:186683600-186694200	Weak transcription	HSMM	muscle
14	chr4:186683800-186691400	Weak transcription	HSMMtube	muscle
15	chr4:186683800-186692600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:186686600-186691400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:186687600-186692800	Weak transcription	HUVEC	blood vessel
18	chr4:186687600-186693200	Weak transcription	Right Ventricle	heart
19	chr4:186689400-186692600	Weak transcription	Aorta	Aorta
20	chr4:186689400-186693000	Weak transcription	HepG2	liver
21	chr4:186689400-186693200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:186689800-186693200	Weak transcription	Left Ventricle	heart
23	chr4:186689800-186693200	Weak transcription	Pancreas	Pancrea
24	chr4:186690400-186692400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:186690400-186693000	Genic enhancers	Fetal Heart	heart
26	chr4:186690400-186693400	Weak transcription	Liver	Liver
27	chr4:186690600-186695600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:186690800-186691600	ZNF genes & repeats	Fetal Intestine Small	intestine

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