Variant report

Variant	rs6659012
Chromosome Location	chr1:227828716-227828717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227824309..227826366-chr1:227826711..227829251,2	K562	blood:
2	chr1:227826740..227828774-chr1:227831005..227833659,2	K562	blood:

Variant related genes	Relation type
ENSG00000265216	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1045407	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753436	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753437	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799422	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799424	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799428	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799437	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799444	0.93[EUR][1000 genomes]
rs10916154	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916157	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916160	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916161	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916162	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916163	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916166	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916167	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916173	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916180	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916189	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916199	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11576992	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11581704	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590390	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12058246	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081818	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084072	0.84[EUR][1000 genomes]
rs12092054	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093031	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12116848	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119889	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120182	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12129704	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12129894	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131114	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132761	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12133625	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138198	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12138229	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140813	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140848	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390401	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495848	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1845757	0.82[EUR][1000 genomes]
rs1995019	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172936	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446171	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999742	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34421331	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3942992	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4379651	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57158394	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61824940	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426470	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426471	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426472	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656661	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659349	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669236	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669277	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6672530	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678802	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679855	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689375	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691443	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692376	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694427	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696239	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698409	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74140304	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418348	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521812	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531801	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7538206	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538893	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540382	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540754	0.83[EUR][1000 genomes]
rs7549475	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551788	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553531	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903691	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951084	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9726691	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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
3	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
4	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
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945342	chr1:227819395-227829907	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3334041	chr1:227828477-227828925	ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6659012	JMJD4	cis	multi-tissue	Pritchard
rs6659012	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227811800-227830600	ZNF genes & repeats	Liver	Liver
4	chr1:227815200-227828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:227818600-227830600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr1:227818600-227834200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr1:227819800-227837600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:227820000-227829200	ZNF genes & repeats	Fetal Stomach	stomach
9	chr1:227820200-227830400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr1:227820200-227831400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr1:227825200-227830400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr1:227826000-227829000	ZNF genes & repeats	Pancreas	Pancrea
14	chr1:227826600-227828800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:227826600-227828800	ZNF genes & repeats	Aorta	Aorta
16	chr1:227826600-227829000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:227827400-227829000	ZNF genes & repeats	Fetal Lung	lung
18	chr1:227827400-227830000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:227827400-227830800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:227827600-227829000	ZNF genes & repeats	Lung	lung
21	chr1:227827600-227829200	ZNF genes & repeats	Dnd41	blood
22	chr1:227827600-227830400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
23	chr1:227827800-227829800	ZNF genes & repeats	Brain Anterior Caudate	brain
24	chr1:227827800-227830600	Weak transcription	Fetal Heart	heart
25	chr1:227827800-227830800	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr1:227828000-227830200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:227828000-227830600	ZNF genes & repeats	Ovary	ovary
29	chr1:227828200-227829000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:227828200-227829200	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr1:227828200-227830400	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr1:227828200-227830800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
33	chr1:227828200-227831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:227828400-227829000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr1:227828400-227830200	ZNF genes & repeats	Left Ventricle	heart
36	chr1:227828400-227837400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
37	chr1:227828600-227829000	ZNF genes & repeats	Gastric	stomach
38	chr1:227828600-227829000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
39	chr1:227828600-227829400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:227828600-227830200	ZNF genes & repeats	Colonic Mucosa	Colon

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