Variant report

Variant	rs1168945
Chromosome Location	chr12:121327716-121327717
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121317330..121318863-chr12:121327465..121328985,2	MCF-7	breast:
2	chr12:121326076..121329274-chr12:121333779..121337730,3	MCF-7	breast:
3	chr12:121326911..121329389-chr12:121341221..121344102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1067742	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774577	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1105416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065286	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1151850	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151851	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1151852	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151861	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151863	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151864	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1168954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1696361	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1696363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718209	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732395	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732396	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1732398	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732405	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2649994	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2649995	0.85[EUR][1000 genomes]
rs2649996	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2649998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2650006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2701174	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2701178	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2701181	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2701182	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2948150	1.00[YRI][hapmap]
rs4767938	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs482522	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs487310	0.89[CHB][hapmap]
rs487912	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs491602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497273	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs509152	1.00[YRI][hapmap]
rs520405	0.85[EUR][1000 genomes]
rs532140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs532703	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs538785	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550349	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs551087	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs564120	0.84[EUR][1000 genomes]
rs566994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs584001	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs586305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs589466	0.81[EUR][1000 genomes]
rs589699	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs594507	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs597203	0.84[EUR][1000 genomes]
rs610578	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs618849	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs619679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs628771	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631168	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs633084	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6553	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs656933	0.93[ASN][1000 genomes]
rs662284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs662739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs674021	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs679833	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs683091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs683437	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs688402	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7300722	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs791210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs791707	0.84[EUR][1000 genomes]
rs791713	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1168945	UNQ1887	cis	Temporal Cortex	GTEx
rs1168945	SPPL3	cis	Adipose Subcutaneous	GTEx
rs1168945	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
2	chr12:121294200-121340400	Weak transcription	HSMM	muscle
3	chr12:121297400-121339800	Weak transcription	A549	lung
4	chr12:121300600-121328800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:121302000-121328800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:121304200-121329800	Weak transcription	K562	blood
7	chr12:121304600-121339800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:121306600-121331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:121310800-121331400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:121312600-121339800	Weak transcription	Brain Germinal Matrix	brain
11	chr12:121312600-121339800	Weak transcription	NHDF-Ad	bronchial
12	chr12:121313000-121332600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:121313400-121330000	Weak transcription	Psoas Muscle	Psoas
14	chr12:121313400-121332400	Weak transcription	Lung	lung
15	chr12:121313400-121339800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:121313400-121339800	Weak transcription	Pancreas	Pancrea
17	chr12:121315400-121332200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:121315800-121331400	Weak transcription	Fetal Stomach	stomach
19	chr12:121317200-121333400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:121317400-121338000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:121317600-121331400	Weak transcription	HepG2	liver
22	chr12:121317600-121339600	Weak transcription	HMEC	breast
23	chr12:121317800-121339600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:121318200-121339600	Weak transcription	NHEK	skin
25	chr12:121318200-121340400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:121320800-121328600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:121320800-121328800	Weak transcription	Liver	Liver
28	chr12:121323200-121340000	Weak transcription	Fetal Lung	lung
29	chr12:121323400-121328800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:121323600-121330000	Weak transcription	Brain Angular Gyrus	brain
31	chr12:121323600-121330000	Weak transcription	Right Ventricle	heart
32	chr12:121323600-121331400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:121323600-121332200	Weak transcription	Stomach Mucosa	stomach
34	chr12:121323600-121340600	Weak transcription	Aorta	Aorta
35	chr12:121324000-121340400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:121324400-121328600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:121324400-121328600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:121324400-121330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:121324400-121330000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:121324400-121331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:121324400-121334000	Weak transcription	Small Intestine	intestine
42	chr12:121324400-121339600	Weak transcription	Brain Substantia Nigra	brain
43	chr12:121324400-121339800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:121324600-121330000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:121324600-121330000	Weak transcription	Dnd41	blood
46	chr12:121324600-121339400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:121324800-121328600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:121324800-121329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:121324800-121329800	Weak transcription	Primary B cells from cord blood	blood
50	chr12:121325000-121330000	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links