Variant report

Variant	rs778368
Chromosome Location	chr2:233745333-233745334
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233744737..233747188-chr2:233755867..233757866,2	MCF-7	breast:
2	chr2:233738116..233740416-chr2:233743291..233745431,2	K562	blood:
3	chr2:233739591..233745527-chr2:233747956..233752237,8	MCF-7	breast:
4	chr2:233740324..233742674-chr2:233744201..233746410,2	MCF-7	breast:
5	chr2:233744358..233746968-chr2:233756848..233759131,3	K562	blood:

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction
ENSG00000066248	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10933411	0.93[ASN][1000 genomes]
rs10933412	0.93[ASN][1000 genomes]
rs11676216	0.93[ASN][1000 genomes]
rs12694917	0.93[ASN][1000 genomes]
rs1446310	0.83[ASN][1000 genomes]
rs1446311	0.92[ASN][1000 genomes]
rs1867778	0.83[ASN][1000 genomes]
rs1947105	0.95[ASN][1000 genomes]
rs2044449	0.95[ASN][1000 genomes]
rs2100053	0.95[ASN][1000 genomes]
rs2250654	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2250665	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305137	0.93[ASN][1000 genomes]
rs2305141	0.83[ASN][1000 genomes]
rs2592102	0.95[ASN][1000 genomes]
rs2592113	0.83[ASN][1000 genomes]
rs2592115	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2592116	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2592117	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2592126	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2674839	0.83[ASN][1000 genomes]
rs2675957	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2675966	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2675967	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2675971	0.95[ASN][1000 genomes]
rs2675973	0.93[ASN][1000 genomes]
rs2675974	0.93[ASN][1000 genomes]
rs283466	0.83[ASN][1000 genomes]
rs283468	0.81[ASN][1000 genomes]
rs283471	0.81[ASN][1000 genomes]
rs3816334	0.93[ASN][1000 genomes]
rs4973053	0.83[ASN][1000 genomes]
rs4973054	0.93[ASN][1000 genomes]
rs4973055	0.93[ASN][1000 genomes]
rs4973056	0.91[ASN][1000 genomes]
rs4973560	0.80[ASN][1000 genomes]
rs4973561	0.83[ASN][1000 genomes]
rs6437074	0.93[ASN][1000 genomes]
rs6719061	0.84[ASN][1000 genomes]
rs709933	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709934	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709938	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558609	0.84[ASN][1000 genomes]
rs7573208	0.84[ASN][1000 genomes]
rs7587309	0.92[ASN][1000 genomes]
rs7589201	0.95[ASN][1000 genomes]
rs778338	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778339	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778340	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs809639	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812383	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs895430	0.95[ASN][1000 genomes]
rs9653383	0.81[ASN][1000 genomes]
rs991873	0.93[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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs778368	C2orf82	cis	intralobular white matter	BrainEAC
rs778368	C2orf82	cis	brain	BrainEAC
rs778368	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
2	chr2:233741600-233747000	Weak transcription	Gastric	stomach
3	chr2:233741600-233747600	Weak transcription	NHLF	lung
4	chr2:233741600-233749600	Weak transcription	Pancreas	Pancrea
5	chr2:233741800-233750000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:233742000-233749000	Weak transcription	Small Intestine	intestine
7	chr2:233742200-233747400	Weak transcription	Fetal Brain Female	brain
8	chr2:233742200-233749800	Weak transcription	Brain Germinal Matrix	brain
9	chr2:233742200-233750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:233742200-233750800	Weak transcription	Fetal Brain Male	brain
11	chr2:233742400-233752400	Weak transcription	Colonic Mucosa	Colon
12	chr2:233742400-233754200	Strong transcription	Fetal Intestine Small	intestine
13	chr2:233742400-233755600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:233742600-233745800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:233742600-233753400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:233742800-233746000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:233742800-233755600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:233743000-233748000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:233743000-233753000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:233743000-233755800	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:233743200-233745800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:233743200-233746200	Genic enhancers	HepG2	liver
23	chr2:233743200-233759600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr2:233744200-233746000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:233744400-233745400	Enhancers	Liver	Liver
26	chr2:233744400-233745800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:233744600-233745600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:233744600-233755400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:233744800-233745600	Weak transcription	Esophagus	oesophagus
30	chr2:233745000-233746600	Weak transcription	Fetal Stomach	stomach
31	chr2:233745200-233746600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:233745200-233747800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:233745200-233748400	Weak transcription	A549	lung
34	chr2:233745200-233753000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:233745200-233755600	Weak transcription	Brain Angular Gyrus	brain
36	chr2:233745200-233755800	Weak transcription	Brain Cingulate Gyrus	brain

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