Variant report

Variant	rs12346816
Chromosome Location	chr9:115955553-115955554
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	chr9:115953587..115956055-chr9:116171770..116173281,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081639	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10081701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118727	0.88[AFR][1000 genomes]
rs10118914	0.88[AFR][1000 genomes]
rs10121981	0.90[ASN][1000 genomes]
rs10122151	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10817454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981672	0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs10981679	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981687	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1128786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12236187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16912536	0.90[AFR][1000 genomes]
rs16927031	0.90[AFR][1000 genomes]
rs17762642	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28574672	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3810910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3934969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68122369	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021999	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029408	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035169	0.90[AFR][1000 genomes]
rs7038260	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758243	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73552213	0.86[AFR][1000 genomes]
rs7849150	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7850672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850723	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851935	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7855105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7856067	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860472	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7865125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9695716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	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
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12346816	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	chr9:115920000-115970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:115920000-115973400	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr9:115920200-115956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:115920400-115973400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:115920800-115966400	Strong transcription	Dnd41	blood
6	chr9:115920800-115975000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:115922800-115956400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr9:115923000-115956200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr9:115923400-115976400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr9:115924000-115965800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:115924200-115969600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:115926000-115956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:115927600-115973400	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:115941200-115968600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr9:115941200-115969200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:115942000-115956400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr9:115942400-115956000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:115943200-115956800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr9:115945400-115977200	Weak transcription	Stomach Mucosa	stomach
21	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:115946000-115963600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:115947800-115956600	Strong transcription	Brain Angular Gyrus	brain
24	chr9:115949800-115961800	Weak transcription	Small Intestine	intestine
25	chr9:115950400-115972800	Weak transcription	Right Ventricle	heart
26	chr9:115950600-115959400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:115950600-115968600	Weak transcription	Fetal Heart	heart
28	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:115950800-115955600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:115950800-115956000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:115950800-115956400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:115950800-115961800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:115950800-115963400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:115950800-115963600	Weak transcription	Spleen	Spleen
35	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:115951000-115955600	Weak transcription	Esophagus	oesophagus
37	chr9:115951000-115956000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:115951000-115957600	Weak transcription	NHLF	lung
39	chr9:115951000-115959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:115951000-115959200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:115951000-115972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:115951000-115972200	Weak transcription	Gastric	stomach
43	chr9:115951000-115972200	Weak transcription	Pancreas	Pancrea
44	chr9:115951000-115974000	Strong transcription	Placenta	Placenta
45	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:115951200-115955600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:115951200-115959000	Weak transcription	Fetal Kidney	kidney
48	chr9:115951200-115959200	Weak transcription	Colonic Mucosa	Colon
49	chr9:115951200-115964800	Weak transcription	Fetal Brain Male	brain
50	chr9:115951400-115959400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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