Variant report

Variant	rs12023488
Chromosome Location	chr1:212498198-212498199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212497077..212499015-chr1:212500342..212502392,2	K562	blood:
2	chr1:212497277..212499052-chr1:212502846..212504617,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM206-3	chr1:212497766-212502930	l_184_chr1:212497765-212519010_heart

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10019	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119904	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12024665	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033246	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035647	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036130	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12410664	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17042034	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1774249	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992643	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2252044	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298114	0.89[ASN][1000 genomes]
rs3099112	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351380	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351393	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351398	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351401	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs351417	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3767861	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767862	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767863	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951588	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951589	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659594	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs701905	0.80[EUR][1000 genomes]
rs7415843	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519959	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521853	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792445	0.92[EUR][1000 genomes];0.85[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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1806604	chr1:212468974-212505860	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12023488	NENF	cis	Esophagus Mucosa	GTEx
rs12023488	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs12023488	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
2	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:212467400-212526000	Weak transcription	A549	lung
5	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
7	chr1:212484000-212503000	Weak transcription	Fetal Stomach	stomach
8	chr1:212484000-212506600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:212484200-212507000	Weak transcription	HepG2	liver
10	chr1:212484400-212502800	Weak transcription	Thymus	Thymus
11	chr1:212484400-212506800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:212484600-212507200	Weak transcription	Right Ventricle	heart
13	chr1:212484800-212503000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:212486000-212504000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:212486000-212507000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:212486200-212526000	Weak transcription	HUVEC	blood vessel
17	chr1:212486600-212502200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:212486600-212506800	Weak transcription	Ovary	ovary
19	chr1:212486800-212503600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:212487200-212506600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:212487800-212502000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:212488000-212502600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:212489000-212502400	Weak transcription	GM12878-XiMat	blood
24	chr1:212489600-212500800	Weak transcription	Pancreas	Pancrea
25	chr1:212489600-212502000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:212489600-212506800	Weak transcription	NHDF-Ad	bronchial
27	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
28	chr1:212489800-212500800	Weak transcription	Left Ventricle	heart
29	chr1:212489800-212503400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:212489800-212505400	Weak transcription	Fetal Lung	lung
31	chr1:212489800-212506800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:212489800-212506800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:212490000-212507800	Weak transcription	Brain Angular Gyrus	brain
34	chr1:212491600-212502800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:212491800-212502600	Weak transcription	Hela-S3	cervix
36	chr1:212492400-212506800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:212492800-212502600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:212492800-212504400	Weak transcription	Adipose Nuclei	Adipose
39	chr1:212493000-212502800	Weak transcription	Primary B cells from cord blood	blood
40	chr1:212493600-212502800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:212493800-212506000	Weak transcription	K562	blood
42	chr1:212493800-212506800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:212493800-212507200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:212495600-212498200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:212495600-212498800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:212495600-212501000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr1:212495800-212500000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:212496000-212502800	Weak transcription	Fetal Intestine Large	intestine
50	chr1:212496200-212500000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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