Variant report

Variant	rs28574672
Chromosome Location	chr9:115922331-115922332
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	chr9:115916286..115919484-chr9:115921664..115924647,3	K562	blood:
2	chr9:115913338..115915206-chr9:115920921..115923373,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10081639	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10081701	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10118429	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10121981	0.93[ASN][1000 genomes]
rs10122151	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817454	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981662	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10981679	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981686	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10981687	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1128786	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12236187	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12346816	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12684417	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16910202	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17762642	0.85[ASN][1000 genomes]
rs3810910	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934969	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68122369	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021999	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7029408	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7038260	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72758243	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7849150	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7850672	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7850723	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7851935	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7854882	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7855105	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7856067	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7860472	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7863351	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7865125	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9695716	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831691	chr9:115754699-115929459	Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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 target site	71 gene(s)	inside rSNPs	diseases
5	nsv1051654	chr9:115881588-115935663	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv466507	chr9:115905850-115936903	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv615213	chr9:115905850-115936903	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28574672	SLC31A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115914000-115923600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:115914000-115925000	Weak transcription	Fetal Kidney	kidney
3	chr9:115914200-115922800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:115914200-115922800	Weak transcription	Fetal Heart	heart
5	chr9:115914200-115923600	Weak transcription	A549	lung
6	chr9:115914200-115923800	Weak transcription	HUVEC	blood vessel
7	chr9:115914400-115925000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:115914800-115926400	Weak transcription	Fetal Brain Male	brain
9	chr9:115915000-115923000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:115915000-115923400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:115915000-115923600	Weak transcription	Colonic Mucosa	Colon
12	chr9:115915200-115923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:115915200-115930200	Weak transcription	Stomach Mucosa	stomach
14	chr9:115915400-115923400	Weak transcription	Hela-S3	cervix
15	chr9:115915400-115925200	Weak transcription	Small Intestine	intestine
16	chr9:115917400-115923000	Weak transcription	NHDF-Ad	bronchial
17	chr9:115917600-115923800	Weak transcription	HepG2	liver
18	chr9:115917800-115949400	Strong transcription	Placenta	Placenta
19	chr9:115918200-115923600	Weak transcription	Psoas Muscle	Psoas
20	chr9:115918400-115923400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:115918400-115947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:115918600-115922800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:115918600-115922800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:115918600-115923000	Weak transcription	GM12878-XiMat	blood
25	chr9:115918600-115923600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr9:115918600-115924400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:115918600-115926400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:115918600-115930200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:115918800-115922400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:115918800-115922600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:115918800-115923800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:115918800-115924000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr9:115918800-115926600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:115918800-115937000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:115919000-115922400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:115919000-115923000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:115919000-115923000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:115919000-115923000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr9:115919000-115923400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:115919000-115923600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr9:115919000-115923800	Weak transcription	K562	blood
42	chr9:115919000-115926600	Strong transcription	NHLF	lung
43	chr9:115919000-115929800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr9:115919000-115935600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr9:115919000-115936800	Strong transcription	Fetal Brain Female	brain
46	chr9:115919200-115923400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr9:115919200-115926400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr9:115919200-115926600	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:115919200-115937400	Strong transcription	HMEC	breast
50	chr9:115919200-115950800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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