Variant report

Variant	rs12684417
Chromosome Location	chr9:115952895-115952896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115952878..115954594-chr9:115956098..115958292,2	K562	blood:
2	chr9:115952251..115954367-chr9:115960312..115963132,2	K562	blood:
3	chr9:115951377..115953931-chr9:115974239..115975925,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10081639	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10081701	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121981	0.90[ASN][1000 genomes]
rs10122151	0.95[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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981662	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981672	0.81[MKK][hapmap]
rs10981679	1.00[AFR][1000 genomes];1.00[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981687	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1128786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12236187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339424	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12344443	0.86[YRI][hapmap];0.93[AFR][1000 genomes]
rs12346816	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];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17762642	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28574672	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3810910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3934969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68122369	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021999	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029408	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034425	0.93[ASW][hapmap];0.81[MKK][hapmap]
rs7038260	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758243	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7849150	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7850672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850723	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851935	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7855105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7856067	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860472	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7865125	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]
rs9695716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12684417	SLC31A1	Cis_1M	lymphoblastoid	RTeQTL
rs12684417	C9orf5	cis	cerebellum	SCAN
rs12684417	SLC31A1	cis	cerebellum	SCAN
rs12684417	ZNF618	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115919400-115954200	Strong transcription	Fetal Intestine Large	intestine
2	chr9:115920000-115970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:115920000-115973400	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr9:115920200-115956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:115920400-115973400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:115920800-115966400	Strong transcription	Dnd41	blood
7	chr9:115920800-115975000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:115922800-115956400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:115923000-115956200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:115923400-115976400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr9:115923600-115953600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr9:115924000-115965800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:115924200-115969600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:115926000-115956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:115927200-115953600	Strong transcription	Fetal Lung	lung
16	chr9:115927600-115973400	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:115938000-115953000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:115938400-115953200	Strong transcription	K562	blood
20	chr9:115938800-115953400	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:115941200-115968600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr9:115941200-115969200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:115942000-115956400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr9:115942400-115956000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:115943200-115956800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr9:115943400-115953000	Strong transcription	Brain Germinal Matrix	brain
27	chr9:115943800-115953200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr9:115944000-115953600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:115945400-115977200	Weak transcription	Stomach Mucosa	stomach
30	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:115946000-115963600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:115947800-115956600	Strong transcription	Brain Angular Gyrus	brain
33	chr9:115949800-115961800	Weak transcription	Small Intestine	intestine
34	chr9:115950400-115972800	Weak transcription	Right Ventricle	heart
35	chr9:115950600-115959400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:115950600-115968600	Weak transcription	Fetal Heart	heart
37	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:115950800-115953000	Weak transcription	Fetal Brain Female	brain
39	chr9:115950800-115955600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:115950800-115956000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:115950800-115956400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:115950800-115961800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:115950800-115963400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr9:115950800-115963600	Weak transcription	Spleen	Spleen
45	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:115951000-115954600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:115951000-115954600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:115951000-115954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:115951000-115954600	Weak transcription	Aorta	Aorta
50	chr9:115951000-115954600	Weak transcription	Brain Cingulate Gyrus	brain

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