Variant report

Variant	rs575025
Chromosome Location	chr1:212623690-212623691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212604148..212606552-chr1:212621916..212623938,2	K562	blood:
2	chr1:212622646..212625445-chr1:212627199..212631249,4	K562	blood:
3	chr1:212617519..212622581-chr1:212622841..212626048,6	K562	blood:
4	chr1:212622374..212624323-chr1:212736768..212739383,2	K562	blood:
5	chr1:212201500..212204262-chr1:212622636..212624940,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000117691	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs3767871	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472463	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs479564	0.96[ASN][1000 genomes]
rs479807	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4804	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs483954	0.83[EUR][1000 genomes]
rs508432	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514362	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521469	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527840	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs534186	0.91[ASN][1000 genomes]
rs577671	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583058	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs595066	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs600016	0.89[EUR][1000 genomes]
rs6540741	0.89[EUR][1000 genomes]
rs676490	0.97[ASN][1000 genomes]
rs681005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694274	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791721	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873157	chr1:212610755-212640982	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv873158	chr1:212610755-212646225	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs575025	TMEM206	cis	Esophagus Mucosa	GTEx
rs575025	NENF	cis	Esophagus Mucosa	GTEx
rs575025	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212607400-212625800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:212607400-212626000	Weak transcription	Colonic Mucosa	Colon
3	chr1:212607400-212629200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:212607600-212624000	Weak transcription	Fetal Brain Male	brain
5	chr1:212607600-212625800	Weak transcription	Stomach Mucosa	stomach
6	chr1:212607600-212626000	Weak transcription	NH-A	brain
7	chr1:212607800-212624400	Weak transcription	NHEK	skin
8	chr1:212607800-212625800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:212607800-212625800	Weak transcription	NHLF	lung
10	chr1:212607800-212629400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:212608000-212625800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:212608000-212627000	Weak transcription	HepG2	liver
13	chr1:212614200-212626000	Weak transcription	Fetal Kidney	kidney
14	chr1:212614400-212626200	Weak transcription	Pancreas	Pancrea
15	chr1:212614400-212629200	Weak transcription	GM12878-XiMat	blood
16	chr1:212614400-212636800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:212616800-212624000	Strong transcription	Fetal Intestine Small	intestine
18	chr1:212618400-212627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:212619000-212625800	Weak transcription	Fetal Lung	lung
20	chr1:212619400-212625800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:212619400-212627000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:212619600-212625600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:212619600-212626000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:212619600-212626000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:212619600-212626400	Weak transcription	Spleen	Spleen
26	chr1:212619600-212629000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:212619600-212629000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:212619600-212629000	Weak transcription	K562	blood
29	chr1:212619600-212629200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:212619600-212636800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:212619800-212624000	Weak transcription	Liver	Liver
32	chr1:212619800-212624200	Weak transcription	Fetal Thymus	thymus
33	chr1:212619800-212625800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:212619800-212629000	Weak transcription	A549	lung
35	chr1:212619800-212629200	Weak transcription	Primary T cells from cord blood	blood
36	chr1:212619800-212629200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:212620000-212623800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:212620000-212624600	Weak transcription	Esophagus	oesophagus
39	chr1:212620000-212625800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:212620000-212625800	Weak transcription	Fetal Brain Female	brain
41	chr1:212620000-212626200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:212620000-212631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:212620200-212625800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:212620200-212629200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:212620200-212629200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:212620200-212631400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:212620600-212624200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:212620600-212625600	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:212620600-212626000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:212620600-212626200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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