Variant report

Variant	rs6542928
Chromosome Location	chr2:100918624-100918625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100906645..100910351-chr2:100915314..100919031,3	K562	blood:
2	chr2:100912722..100916379-chr2:100917427..100921061,4	K562	blood:
3	chr2:100901888..100904596-chr2:100917454..100919195,2	MCF-7	breast:
4	chr2:100916821..100918833-chr2:100924973..100926771,2	K562	blood:
5	chr2:100917463..100919902-chr2:100937056..100939275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10165326	0.85[ASN][1000 genomes]
rs10169580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10178929	1.00[EUR][1000 genomes]
rs10183462	1.00[EUR][1000 genomes]
rs10186689	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187094	1.00[EUR][1000 genomes]
rs10188009	1.00[ASN][1000 genomes]
rs10188619	1.00[EUR][1000 genomes]
rs10190243	1.00[EUR][1000 genomes]
rs10191099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191655	1.00[EUR][1000 genomes]
rs10192741	1.00[ASN][1000 genomes]
rs10193186	1.00[EUR][1000 genomes]
rs10194087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194280	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197013	1.00[EUR][1000 genomes]
rs10205784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207091	1.00[EUR][1000 genomes]
rs10207566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210458	1.00[ASN][1000 genomes]
rs1107428	1.00[EUR][1000 genomes]
rs11123831	1.00[EUR][1000 genomes]
rs11899975	0.85[ASN][1000 genomes]
rs11902829	0.89[ASN][1000 genomes]
rs12329351	1.00[EUR][1000 genomes]
rs13391540	1.00[EUR][1000 genomes]
rs13407391	1.00[EUR][1000 genomes]
rs13413021	1.00[EUR][1000 genomes]
rs13415850	1.00[ASN][1000 genomes]
rs13416287	1.00[EUR][1000 genomes]
rs13417574	1.00[EUR][1000 genomes]
rs13425645	1.00[EUR][1000 genomes]
rs13427376	1.00[EUR][1000 genomes]
rs1465829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17024023	0.85[ASN][1000 genomes]
rs17024153	0.85[ASN][1000 genomes]
rs17024203	1.00[CHB][hapmap]
rs17024207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1992174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309799	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs28485289	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28549897	1.00[EUR][1000 genomes]
rs28631885	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651883	0.89[ASN][1000 genomes]
rs2871338	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs28757637	1.00[EUR][1000 genomes]
rs3748934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4149522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4597550	1.00[EUR][1000 genomes]
rs56377332	1.00[EUR][1000 genomes]
rs57231149	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57699256	0.85[ASN][1000 genomes]
rs58552292	0.92[ASN][1000 genomes]
rs58742261	0.92[ASN][1000 genomes]
rs59193721	1.00[ASN][1000 genomes]
rs59388202	0.81[ASN][1000 genomes]
rs59494003	0.89[ASN][1000 genomes]
rs60292856	1.00[EUR][1000 genomes]
rs60458261	1.00[ASN][1000 genomes]
rs61429123	1.00[ASN][1000 genomes]
rs6542927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6542935	1.00[EUR][1000 genomes]
rs6723222	1.00[EUR][1000 genomes]
rs6728575	0.85[CHD][hapmap]
rs6733677	1.00[EUR][1000 genomes]
rs6734881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742048	1.00[EUR][1000 genomes]
rs6743560	1.00[EUR][1000 genomes]
rs6755284	1.00[EUR][1000 genomes]
rs6759686	1.00[EUR][1000 genomes]
rs72954123	1.00[EUR][1000 genomes]
rs72960174	0.82[ASN][1000 genomes]
rs72966498	1.00[EUR][1000 genomes]
rs72968866	1.00[EUR][1000 genomes]
rs73964443	1.00[EUR][1000 genomes]
rs73968406	1.00[EUR][1000 genomes]
rs7563954	1.00[EUR][1000 genomes]
rs7564318	1.00[EUR][1000 genomes]
rs7567130	1.00[CHB][hapmap]
rs7569334	1.00[EUR][1000 genomes]
rs7585806	1.00[EUR][1000 genomes]
rs7609272	1.00[EUR][1000 genomes]
rs876439	0.85[CHD][hapmap]
rs9808480	1.00[EUR][1000 genomes]
rs995110	1.00[EUR][1000 genomes]
rs995132	1.00[EUR][1000 genomes]
rs995133	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.93[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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
2	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
3	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
4	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
5	chr2:100903600-100926200	Weak transcription	Fetal Kidney	kidney
6	chr2:100908000-100919400	Weak transcription	Spleen	Spleen
7	chr2:100908800-100926600	Weak transcription	Gastric	stomach
8	chr2:100909000-100920600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:100910200-100920000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:100910200-100920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:100910400-100925800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:100910800-100933600	Weak transcription	K562	blood
13	chr2:100912000-100919400	Strong transcription	Brain Anterior Caudate	brain
14	chr2:100912800-100934800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:100915400-100919800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:100915800-100923600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:100915800-100930600	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:100916000-100923600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:100916400-100925800	Strong transcription	A549	lung
20	chr2:100916600-100921400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:100917000-100919400	Strong transcription	Ovary	ovary
22	chr2:100917800-100919800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:100917800-100919800	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr2:100918000-100919800	Enhancers	Liver	Liver
25	chr2:100918000-100920600	Weak transcription	Lung	lung
26	chr2:100918200-100919600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:100918200-100920200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:100918200-100923800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:100918200-100926400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:100918200-100926600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:100918200-100926600	Weak transcription	Left Ventricle	heart
32	chr2:100918200-100929400	Weak transcription	Pancreas	Pancrea
33	chr2:100918200-100937600	Weak transcription	Aorta	Aorta
34	chr2:100918400-100920600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:100918400-100931800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:100918600-100919200	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr2:100918600-100920600	Weak transcription	Brain Germinal Matrix	brain

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