Variant report

Variant	rs7028143
Chromosome Location	chr9:115915859-115915860
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115905644..115908349-chr9:115914691..115916468,2	K562	blood:
2	chr9:115913327..115916086-chr9:115970304..115972231,2	MCF-7	breast:
3	chr9:115873156..115875899-chr9:115915858..115921312,4	MCF-7	breast:
4	chr9:115882894..115884462-chr9:115915677..115917990,2	MCF-7	breast:
5	chr9:115913111..115914699-chr9:115915133..115916997,2	K562	blood:
6	chr9:115887611..115890231-chr9:115913519..115916345,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231528	Chromatin interaction
ENSG00000225684	Chromatin interaction
ENSG00000136867	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10121117	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817447	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10981663	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11791765	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11794048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4599885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851648	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7852229	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[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	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	nsv893743	chr9:115867276-115917783	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv615212	chr9:115891009-115915859	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv8563	chr9:115914276-115917151	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7028143	SLC31A2	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115913000-115916600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:115913800-115918000	Weak transcription	Aorta	Aorta
3	chr9:115914000-115923600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:115914000-115925000	Weak transcription	Fetal Kidney	kidney
5	chr9:115914200-115917200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:115914200-115917600	Weak transcription	Primary T cells from cord blood	blood
7	chr9:115914200-115917600	Enhancers	NHLF	lung
8	chr9:115914200-115917800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:115914200-115919400	Weak transcription	Fetal Stomach	stomach
10	chr9:115914200-115919600	Weak transcription	Fetal Lung	lung
11	chr9:115914200-115919600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:115914200-115920200	Weak transcription	Brain Germinal Matrix	brain
13	chr9:115914200-115922800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:115914200-115922800	Weak transcription	Fetal Heart	heart
15	chr9:115914200-115923600	Weak transcription	A549	lung
16	chr9:115914200-115923800	Weak transcription	HUVEC	blood vessel
17	chr9:115914400-115917200	Enhancers	Left Ventricle	heart
18	chr9:115914400-115917400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:115914400-115917600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:115914400-115917800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr9:115914400-115919200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr9:115914400-115920200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:115914400-115925000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:115914600-115916400	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr9:115914600-115916600	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:115914600-115917400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr9:115914600-115917400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr9:115914600-115918000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr9:115914600-115918200	Weak transcription	Thymus	Thymus
30	chr9:115914600-115920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:115914800-115916000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr9:115914800-115916000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:115914800-115916200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:115914800-115916400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:115914800-115917400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:115914800-115917600	Enhancers	Placenta	Placenta
37	chr9:115914800-115917800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr9:115914800-115917800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr9:115914800-115918200	Weak transcription	K562	blood
40	chr9:115914800-115919400	Weak transcription	Fetal Intestine Large	intestine
41	chr9:115914800-115920600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:115914800-115926400	Weak transcription	Fetal Brain Male	brain
43	chr9:115915000-115916000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:115915000-115916600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:115915000-115916600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:115915000-115916600	Weak transcription	Fetal Thymus	thymus
47	chr9:115915000-115916600	Weak transcription	Ovary	ovary
48	chr9:115915000-115917000	Weak transcription	Liver	Liver
49	chr9:115915000-115917200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:115915000-115917200	Enhancers	Pancreas	Pancrea

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