Variant report

Variant	rs2644143
Chromosome Location	chr1:227731157-227731158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227725436..227728346-chr1:227728933..227731230,4	MCF-7	breast:
2	chr1:227728970..227731707-chr1:227751101..227754291,3	MCF-7	breast:
3	chr1:227726703..227728573-chr1:227729012..227731358,2	K562	blood:
4	chr1:227729010..227735281-chr1:227748522..227752811,6	MCF-7	breast:
5	chr1:227725578..227727494-chr1:227729728..227731720,2	MCF-7	breast:
6	chr1:227728577..227730296-chr1:227730401..227732480,2	MCF-7	breast:
7	chr1:227729455..227731523-chr1:227733555..227735249,2	K562	blood:

Variant related genes	Relation type
ENSG00000202264	Chromatin interaction
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10047205	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916178	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916192	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12059899	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12069550	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12070539	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12080590	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12082414	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12092295	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12095502	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12096675	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1495846	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1495849	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16847966	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16847991	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16847992	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16848029	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1923821	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2012432	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2132366	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2256599	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2453682	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644144	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2644146	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2644153	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644161	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814059	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814060	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814061	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814084	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814085	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2819496	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819498	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2819507	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2819511	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3748806	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4376731	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4589104	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58020705	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59034043	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59149651	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59753688	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61343450	0.82[EUR][1000 genomes]
rs66471275	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66491073	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6659745	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66736638	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6688145	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6693348	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66938123	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67216605	0.82[EUR][1000 genomes]
rs67511833	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67676707	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs68046179	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68186506	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72632830	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72632831	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72632832	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72748074	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7413796	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs753541	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7539151	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903692	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903694	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903695	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965942	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[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	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	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2644143	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs2644143	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227729400-227731200	Enhancers	Fetal Brain Male	brain
2	chr1:227730200-227731400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:227730400-227731200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:227730400-227731200	Weak transcription	Gastric	stomach
5	chr1:227730400-227731200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:227730400-227731200	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr1:227730400-227731600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:227730400-227731600	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:227730400-227735000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227730600-227731200	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr1:227730600-227731200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr1:227730600-227731400	Enhancers	Primary B cells from cord blood	blood
13	chr1:227730600-227731600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:227730600-227731600	Enhancers	Fetal Heart	heart
15	chr1:227730600-227734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:227730800-227731200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:227730800-227731200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:227730800-227731200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:227730800-227731200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:227730800-227731200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:227730800-227731200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:227730800-227731200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:227730800-227731200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:227730800-227731200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:227730800-227731200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:227730800-227731200	Enhancers	Brain Germinal Matrix	brain
27	chr1:227730800-227731200	Enhancers	Fetal Intestine Large	intestine
28	chr1:227730800-227731200	Enhancers	Fetal Intestine Small	intestine
29	chr1:227730800-227731200	Enhancers	Left Ventricle	heart
30	chr1:227730800-227731200	Enhancers	Ovary	ovary
31	chr1:227730800-227731200	Enhancers	Psoas Muscle	Psoas
32	chr1:227730800-227731200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:227730800-227731200	Enhancers	Right Ventricle	heart
34	chr1:227730800-227731400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:227730800-227731400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:227730800-227731400	Enhancers	Colon Smooth Muscle	Colon
37	chr1:227730800-227731400	Enhancers	Fetal Lung	lung
38	chr1:227730800-227731400	Enhancers	Placenta	Placenta
39	chr1:227730800-227731600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:227730800-227731600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr1:227730800-227731600	Enhancers	Fetal Brain Female	brain
42	chr1:227730800-227731600	Bivalent Enhancer	Fetal Stomach	stomach
43	chr1:227730800-227731600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:227730800-227734000	Weak transcription	Spleen	Spleen
45	chr1:227730800-227736000	Enhancers	Fetal Muscle Trunk	muscle
46	chr1:227730800-227736000	Enhancers	Fetal Muscle Leg	muscle
47	chr1:227730800-227736000	Enhancers	Pancreas	Pancrea
48	chr1:227731000-227731200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr1:227731000-227731200	Enhancers	Brain Anterior Caudate	brain
50	chr1:227731000-227731200	Enhancers	Duodenum Smooth Muscle	Duodenum

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