Variant report

Variant	rs57158394
Chromosome Location	chr1:227753578-227753579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227749843..227751616-chr1:227752949..227754872,2	K562	blood:
2	chr1:227751959..227755569-chr1:227762720..227764448,3	MCF-7	breast:
3	chr1:227746809..227749278-chr1:227751802..227753794,2	K562	blood:
4	chr1:227695645..227697944-chr1:227752053..227753592,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction
ENSG00000202264	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1045407	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753436	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753437	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799422	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799424	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799428	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799437	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799444	0.88[EUR][1000 genomes]
rs10916154	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916157	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916160	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916161	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916162	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916163	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916166	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916167	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916173	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916180	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916189	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916199	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11576992	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11581704	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590390	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12058246	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12081818	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12084072	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12092054	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093031	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12116848	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12119889	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12120182	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12123996	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12129704	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12129894	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12131114	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12132761	0.81[EUR][1000 genomes]
rs12133625	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138198	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138229	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12140813	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12140848	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1390401	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1495848	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1845757	0.87[EUR][1000 genomes]
rs1995019	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2172936	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28446171	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2999742	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34421331	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3942992	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4379651	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59885016	0.81[EUR][1000 genomes]
rs61824940	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426470	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426471	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426472	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656661	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659012	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659349	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669236	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6669277	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6672530	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6678802	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6679855	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6689375	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691443	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6692376	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694427	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698409	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74140304	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7418348	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521812	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531801	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7538206	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7538893	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7540382	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549475	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7551788	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553531	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs903691	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs951084	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9726691	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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
rs57158394	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227751800-227756400	Weak transcription	Spleen	Spleen
2	chr1:227752000-227753600	Weak transcription	Placenta	Placenta
3	chr1:227752000-227754000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227752000-227755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:227752000-227756200	Weak transcription	Gastric	stomach
6	chr1:227752000-227756400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:227752000-227756400	Weak transcription	Lung	lung
8	chr1:227752000-227757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227752000-227759800	Weak transcription	Left Ventricle	heart
10	chr1:227752000-227760000	Weak transcription	Esophagus	oesophagus
11	chr1:227752000-227766800	Weak transcription	Ovary	ovary
12	chr1:227752200-227754000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:227752200-227754200	Weak transcription	Brain Angular Gyrus	brain
14	chr1:227752200-227755000	Weak transcription	Colonic Mucosa	Colon
15	chr1:227752200-227755600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:227752200-227756200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:227752200-227756400	Weak transcription	Right Ventricle	heart
18	chr1:227752200-227758200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:227752200-227758800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:227752200-227760000	Weak transcription	Fetal Intestine Large	intestine
21	chr1:227752200-227763200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
23	chr1:227752400-227753600	Weak transcription	A549	lung
24	chr1:227752400-227753600	Weak transcription	NH-A	brain
25	chr1:227752400-227753800	Weak transcription	Primary B cells from cord blood	blood
26	chr1:227752400-227753800	Weak transcription	Fetal Intestine Small	intestine
27	chr1:227752400-227753800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:227752400-227754000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:227752400-227754000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:227752400-227754000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:227752400-227754000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:227752400-227754600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:227752400-227755000	Weak transcription	Fetal Thymus	thymus
34	chr1:227752400-227755000	Weak transcription	HepG2	liver
35	chr1:227752400-227755200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:227752400-227755400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:227752400-227755600	Weak transcription	HSMM	muscle
38	chr1:227752400-227755800	Weak transcription	NHLF	lung
39	chr1:227752400-227756000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:227752400-227756200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:227752400-227756600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:227752400-227756600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:227752400-227757000	Weak transcription	NHDF-Ad	bronchial
44	chr1:227752400-227757400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:227752400-227757600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:227752400-227757800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227752400-227758000	Weak transcription	Osteobl	bone
48	chr1:227752400-227758200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:227752400-227759600	Weak transcription	Primary T cells from cord blood	blood
50	chr1:227752400-227759800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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