Variant report

Variant	rs4973056
Chromosome Location	chr2:233720765-233720766
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233718747..233721195-chr2:233739354..233741020,2	MCF-7	breast:
2	chr2:233720253..233722044-chr2:234158922..234161619,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1044480	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10933409	0.82[EUR][1000 genomes]
rs10933411	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10933412	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11676216	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12694917	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987513	0.80[EUR][1000 genomes]
rs13021246	0.80[EUR][1000 genomes]
rs1446308	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1446310	0.85[ASN][1000 genomes]
rs1446311	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1801251	0.82[EUR][1000 genomes]
rs1867778	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1947105	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2044449	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2100053	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2250654	0.91[ASN][1000 genomes]
rs2250665	0.91[ASN][1000 genomes]
rs2305137	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305141	0.85[ASN][1000 genomes]
rs2592102	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2592105	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2592113	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2592115	0.95[ASN][1000 genomes]
rs2592116	0.95[ASN][1000 genomes]
rs2592117	0.95[ASN][1000 genomes]
rs2592126	0.91[ASN][1000 genomes]
rs2674839	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2675957	0.90[ASN][1000 genomes]
rs2675966	0.95[ASN][1000 genomes]
rs2675967	0.95[ASN][1000 genomes]
rs2675971	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2675973	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2675974	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283466	0.85[ASN][1000 genomes]
rs283468	0.83[ASN][1000 genomes]
rs283469	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs283471	0.83[ASN][1000 genomes]
rs283474	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs283475	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs283476	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs283484	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs283486	0.82[EUR][1000 genomes]
rs33980184	0.80[EUR][1000 genomes]
rs35085837	0.80[EUR][1000 genomes]
rs3816334	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4973053	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4973054	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4973055	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4973560	0.83[ASN][1000 genomes]
rs4973561	0.85[ASN][1000 genomes]
rs56777991	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6437074	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6719061	0.86[ASN][1000 genomes]
rs6748027	0.82[EUR][1000 genomes]
rs709933	0.95[ASN][1000 genomes]
rs709934	0.95[ASN][1000 genomes]
rs709938	0.89[ASN][1000 genomes]
rs737028	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7558609	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568385	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7573208	0.86[ASN][1000 genomes]
rs7587309	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7589201	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778166	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778338	0.95[ASN][1000 genomes]
rs778339	0.93[ASN][1000 genomes]
rs778340	0.95[ASN][1000 genomes]
rs778368	0.91[ASN][1000 genomes]
rs809639	0.95[ASN][1000 genomes]
rs812383	0.95[ASN][1000 genomes]
rs895430	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9653383	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs991873	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4973056	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:233698400-233723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr2:233703400-233726400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:233703400-233726600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:233703600-233725200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:233703800-233724800	Strong transcription	Dnd41	blood
10	chr2:233704000-233721400	Strong transcription	Fetal Intestine Large	intestine
11	chr2:233704200-233725000	Strong transcription	Fetal Thymus	thymus
12	chr2:233704400-233726200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:233704400-233726600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:233704600-233726000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:233704600-233728000	Strong transcription	Primary T cells from cord blood	blood
16	chr2:233704800-233726600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:233705000-233726600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:233705600-233726600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:233705600-233727800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:233712000-233721400	Strong transcription	Fetal Intestine Small	intestine
21	chr2:233712000-233728200	Strong transcription	Fetal Stomach	stomach
22	chr2:233713400-233721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:233713600-233721600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:233714000-233726400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:233714800-233721400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:233714800-233721400	Weak transcription	Fetal Brain Male	brain
27	chr2:233715200-233721200	Weak transcription	Right Ventricle	heart
28	chr2:233715200-233721400	Weak transcription	Stomach Mucosa	stomach
29	chr2:233715800-233721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:233715800-233725400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:233716000-233721200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:233716800-233720800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:233716800-233721000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:233717000-233720800	Weak transcription	Spleen	Spleen
35	chr2:233717000-233721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:233717000-233721000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:233717000-233721200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:233717000-233721200	Weak transcription	Left Ventricle	heart
39	chr2:233717000-233721200	Weak transcription	Pancreas	Pancrea
40	chr2:233717000-233721200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:233717000-233721400	Weak transcription	Aorta	Aorta
42	chr2:233717000-233721400	Weak transcription	Gastric	stomach
43	chr2:233717000-233721600	Weak transcription	Esophagus	oesophagus
44	chr2:233717000-233721600	Enhancers	HSMMtube	muscle
45	chr2:233717400-233721400	Enhancers	Liver	Liver
46	chr2:233717600-233721000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:233717600-233721200	Weak transcription	Colonic Mucosa	Colon
48	chr2:233717800-233721600	Weak transcription	Fetal Kidney	kidney
49	chr2:233717800-233721600	Enhancers	Hela-S3	cervix
50	chr2:233718000-233721600	Enhancers	Muscle Satellite Cultured Cells	--

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