Variant report

Variant	rs12131517
Chromosome Location	chr1:227752581-227752582
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227745812..227749133-chr1:227750205..227753010,3	K562	blood:
2	chr1:227751314..227753059-chr1:227774179..227776637,2	K562	blood:
3	chr1:227751959..227755569-chr1:227762720..227764448,3	MCF-7	breast:
4	chr1:227746809..227749278-chr1:227751802..227753794,2	K562	blood:
5	chr1:227750211..227752851-chr1:227914757..227917634,3	MCF-7	breast:
6	chr1:227750240..227752795-chr1:227921793..227923560,2	K562	blood:
7	chr1:227751815..227753395-chr1:227758245..227760827,2	K562	blood:
8	chr1:227126771..227129566-chr1:227749760..227753054,3	K562	blood:
9	chr1:227695645..227697944-chr1:227752053..227753592,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000202264	Chromatin interaction
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10495277	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799429	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799438	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1080061	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916172	0.98[ASN][1000 genomes]
rs10916177	0.97[ASN][1000 genomes]
rs1154835	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11805477	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11806830	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11807529	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12120313	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12122398	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124325	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126339	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12133008	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12135976	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12137033	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12138942	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12141938	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12408514	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1390400	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16848036	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1874371	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1923822	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1951729	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2012386	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2031134	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2093608	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2313245	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999750	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3010188	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34901559	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4306097	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653509	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653851	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653862	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653864	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653865	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55721361	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55841672	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56197655	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56349581	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57346808	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58274339	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59336221	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60625678	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61322441	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61566561	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426469	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6667937	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699448	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528010	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9725624	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12131517	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227750600-227752600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:227751000-227752600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:227751000-227752600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:227751600-227752600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:227751800-227752600	Flanking Active TSS	Dnd41	blood
6	chr1:227751800-227756400	Weak transcription	Spleen	Spleen
7	chr1:227752000-227752600	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:227752000-227752600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:227752000-227752600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:227752000-227752600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:227752000-227752600	Flanking Active TSS	Fetal Brain Female	brain
12	chr1:227752000-227752600	Flanking Active TSS	K562	blood
13	chr1:227752000-227753600	Weak transcription	Placenta	Placenta
14	chr1:227752000-227754000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:227752000-227755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:227752000-227756200	Weak transcription	Gastric	stomach
17	chr1:227752000-227756400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:227752000-227756400	Weak transcription	Lung	lung
19	chr1:227752000-227757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:227752000-227759800	Weak transcription	Left Ventricle	heart
21	chr1:227752000-227760000	Weak transcription	Esophagus	oesophagus
22	chr1:227752000-227766800	Weak transcription	Ovary	ovary
23	chr1:227752200-227752600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:227752200-227752600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:227752200-227752600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:227752200-227752600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr1:227752200-227752600	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:227752200-227753200	Enhancers	Primary T cells fromperipheralblood	blood
29	chr1:227752200-227753200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:227752200-227753200	Enhancers	Psoas Muscle	Psoas
31	chr1:227752200-227753400	Enhancers	Thymus	Thymus
32	chr1:227752200-227754000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:227752200-227754200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:227752200-227755000	Weak transcription	Colonic Mucosa	Colon
35	chr1:227752200-227755600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:227752200-227756200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:227752200-227756400	Weak transcription	Right Ventricle	heart
38	chr1:227752200-227758200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:227752200-227758800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:227752200-227760000	Weak transcription	Fetal Intestine Large	intestine
41	chr1:227752200-227763200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
43	chr1:227752400-227752600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:227752400-227752600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:227752400-227752600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:227752400-227752600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:227752400-227752600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr1:227752400-227752600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:227752400-227752600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:227752400-227752600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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