Variant report

Variant	rs28641923
Chromosome Location	chr17:18114912-18114913
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18111005..18113844-chr17:18114465..18116043,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11869205	0.96[ASN][1000 genomes]
rs11870766	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11871970	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12150618	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12451754	0.98[ASN][1000 genomes]
rs12936694	0.96[ASN][1000 genomes]
rs12939469	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12946842	0.93[ASN][1000 genomes]
rs1378601	0.90[ASN][1000 genomes]
rs1378602	0.90[ASN][1000 genomes]
rs2360234	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2925137	0.96[ASN][1000 genomes]
rs2925138	0.96[ASN][1000 genomes]
rs4603612	0.93[ASN][1000 genomes]
rs4924839	0.90[ASN][1000 genomes]
rs4924840	0.98[ASN][1000 genomes]
rs4924841	0.98[ASN][1000 genomes]
rs4925149	0.95[ASN][1000 genomes]
rs4925150	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56021431	0.96[ASN][1000 genomes]
rs712270	0.84[ASN][1000 genomes]
rs712273	0.85[ASN][1000 genomes]
rs712275	0.91[ASN][1000 genomes]
rs7212808	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8069321	0.80[ASN][1000 genomes]
rs8071834	0.88[ASN][1000 genomes]
rs854795	0.85[ASN][1000 genomes]
rs854797	0.89[ASN][1000 genomes]
rs854798	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs854799	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs854801	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs854804	0.85[ASN][1000 genomes]
rs854805	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs854806	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs854807	0.93[ASN][1000 genomes]
rs860568	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28641923	RP11-258F1.1	cis	Adipose Subcutaneous	GTEx
rs28641923	ALKBH5	cis	Esophagus Muscularis	GTEx
rs28641923	LGALS9C	cis	Whole Blood	GTEx
rs28641923	ALKBH5	cis	Artery Tibial	GTEx
rs28641923	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs28641923	LLGL1	cis	Esophagus Mucosa	GTEx
rs28641923	SHMT1	cis	Esophagus Muscularis	GTEx
rs28641923	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18095400-18116000	Strong transcription	Fetal Stomach	stomach
2	chr17:18101600-18115400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:18102000-18116200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr17:18104800-18116400	Weak transcription	Psoas Muscle	Psoas
5	chr17:18107200-18115400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:18107400-18115200	Strong transcription	Fetal Intestine Small	intestine
7	chr17:18109000-18115200	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr17:18109000-18115800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:18109400-18116600	Weak transcription	Fetal Kidney	kidney
10	chr17:18109400-18117000	Weak transcription	Fetal Brain Male	brain
11	chr17:18109400-18122200	Weak transcription	K562	blood
12	chr17:18109600-18117600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:18110400-18115800	Strong transcription	Pancreas	Pancrea
14	chr17:18110600-18122200	Weak transcription	NHDF-Ad	bronchial
15	chr17:18112600-18127400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:18113000-18128200	Weak transcription	Small Intestine	intestine
17	chr17:18113200-18116800	Weak transcription	HepG2	liver
18	chr17:18113200-18128200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr17:18113600-18121200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:18113600-18128000	Weak transcription	Colon Smooth Muscle	Colon
21	chr17:18113800-18116400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:18113800-18116800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:18113800-18122000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr17:18113800-18124400	Weak transcription	Hela-S3	cervix
25	chr17:18113800-18124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:18113800-18127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr17:18113800-18127400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:18113800-18128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr17:18114000-18120800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:18114000-18121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:18114200-18115000	Weak transcription	Stomach Mucosa	stomach
32	chr17:18114200-18117000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr17:18114200-18117600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:18114200-18118200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr17:18114200-18122000	Weak transcription	NH-A	brain
36	chr17:18114200-18122200	Weak transcription	Fetal Lung	lung
37	chr17:18114200-18122200	Weak transcription	HUVEC	blood vessel
38	chr17:18114200-18127400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:18114200-18127400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:18114200-18127400	Weak transcription	Left Ventricle	heart
41	chr17:18114400-18117000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:18114400-18117600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr17:18114400-18117600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr17:18114400-18117600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:18114400-18117600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:18114400-18117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:18114400-18117800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:18114400-18118200	Weak transcription	Primary T cells from cord blood	blood
49	chr17:18114400-18118200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr17:18114400-18120800	Weak transcription	Primary T cells fromperipheralblood	blood

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