Variant report

Variant	rs4959180
Chromosome Location	chr6:2387890-2387891
allele	C/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	BATF	chr6:2387834-2388054	GM12878	blood:	n/a	chr6:2387979-2387990
2	RUNX3	chr6:2387800-2388081	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:2387794-2388062	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
GMDS-AS1	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11965611	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11968173	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12524370	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12529088	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13191094	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13198172	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13200914	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13204171	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13214285	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13220248	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17536894	0.85[EUR][1000 genomes]
rs17608626	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17609498	0.84[EUR][1000 genomes]
rs28360628	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34172338	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34610626	0.85[EUR][1000 genomes]
rs34854900	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34901328	0.85[EUR][1000 genomes]
rs34932214	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34996746	0.81[EUR][1000 genomes]
rs35182831	0.84[EUR][1000 genomes]
rs35590232	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35892674	0.85[EUR][1000 genomes]
rs35918040	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3734504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3734505	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3734507	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823107	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4596531	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959175	0.83[EUR][1000 genomes]
rs4959176	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4959177	0.87[AMR][1000 genomes]
rs4959181	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959182	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959658	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959661	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959662	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959663	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959665	0.82[AMR][1000 genomes]
rs55939357	0.80[EUR][1000 genomes]
rs56343276	0.85[EUR][1000 genomes]
rs59493792	0.85[EUR][1000 genomes]
rs62391186	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902556	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6908555	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6911665	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71552124	0.84[EUR][1000 genomes]
rs7738954	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7755646	0.84[AMR][1000 genomes]
rs7773388	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9501836	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9501838	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503185	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503186	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503187	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503188	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503189	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9791368	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2362400-2391800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:2362400-2397200	Weak transcription	Liver	Liver
3	chr6:2362800-2397200	Weak transcription	Left Ventricle	heart
4	chr6:2370200-2389000	Weak transcription	Esophagus	oesophagus
5	chr6:2376800-2389000	Weak transcription	Pancreas	Pancrea
6	chr6:2381000-2397200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:2382800-2397000	Weak transcription	Fetal Stomach	stomach
8	chr6:2383000-2396800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:2383000-2397600	Weak transcription	Gastric	stomach
10	chr6:2383200-2391800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:2383200-2398800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:2383800-2391600	Weak transcription	Aorta	Aorta
13	chr6:2386200-2391400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:2387000-2396800	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:2387400-2389000	Weak transcription	Lung	lung
16	chr6:2387600-2398200	Weak transcription	Ovary	ovary
17	chr6:2387800-2390600	Weak transcription	Primary T cells from cord blood	blood
18	chr6:2387800-2397400	Weak transcription	Adipose Nuclei	Adipose

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