Variant report

Variant	rs869781
Chromosome Location	chr12:121340246-121340247
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	chr12:121338472..121340356-chr12:121340571..121343275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065284	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065293	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065307	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065332	0.86[ASN][1000 genomes]
rs1151849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151859	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11608262	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611087	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168944	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168946	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168948	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168953	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179939	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12371178	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12372231	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12580949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12809299	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12822123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12824150	0.85[CEU][hapmap]
rs12825746	0.82[ASN][1000 genomes]
rs12831094	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1542859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1696390	0.88[ASN][1000 genomes]
rs1718188	0.89[ASN][1000 genomes]
rs2047568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2062507	0.85[CEU][hapmap]
rs2393716	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2650017	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2701177	0.89[ASN][1000 genomes]
rs2701184	0.91[ASN][1000 genomes]
rs2893876	0.80[EUR][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs34009825	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34076777	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35600816	0.80[ASN][1000 genomes]
rs35706672	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35905305	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809313	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3842985	0.81[EUR][1000 genomes]
rs3861797	0.81[EUR][1000 genomes]
rs3883901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3897746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3901854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs4454799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4766979	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4766980	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767935	0.85[CEU][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4767941	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs487943	0.91[ASN][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520753	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs533264	0.90[ASN][1000 genomes]
rs548452	0.92[ASN][1000 genomes]
rs572016	0.81[ASN][1000 genomes]
rs577961	0.81[ASN][1000 genomes]
rs58291418	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58918988	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs590625	0.81[ASN][1000 genomes]
rs602984	0.90[ASN][1000 genomes]
rs609700	0.90[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs61946382	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61946383	0.88[ASN][1000 genomes]
rs61946384	0.90[ASN][1000 genomes]
rs61946385	0.88[ASN][1000 genomes]
rs61946386	0.88[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs647881	0.90[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs665585	0.92[ASN][1000 genomes]
rs666976	0.90[ASN][1000 genomes]
rs7137504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs73413868	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73415720	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73415734	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7967190	0.84[ASN][1000 genomes]
rs7969140	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980311	0.91[ASN][1000 genomes]
rs904628	0.83[ASN][1000 genomes]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs989986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs989987	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv560439	chr12:121340246-121341529	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs869781	ACADS	cis	Thyroid	GTEx
rs869781	HPD	cis	parietal	SCAN
rs869781	SPPL3	cis	cerebellum	SCAN
rs869781	SPPL3	cis	Nerve Tibial	GTEx
rs869781	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs869781	SPPL3	cis	parietal	SCAN
rs869781	SRRM4	cis	cerebellum	SCAN
rs869781	WSB2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121294200-121340400	Weak transcription	HSMM	muscle
2	chr12:121318200-121340400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:121323600-121340600	Weak transcription	Aorta	Aorta
4	chr12:121324000-121340400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:121329000-121340400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:121332000-121340600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:121332400-121340600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:121333200-121340400	Weak transcription	Gastric	stomach
9	chr12:121335800-121340400	Weak transcription	NH-A	brain
10	chr12:121338000-121340600	Enhancers	Small Intestine	intestine
11	chr12:121338200-121340400	Weak transcription	Placenta	Placenta
12	chr12:121338200-121340600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:121338400-121340400	Weak transcription	Esophagus	oesophagus
14	chr12:121338400-121340400	Weak transcription	Lung	lung
15	chr12:121338400-121340600	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:121338600-121340400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:121338600-121340400	Weak transcription	Thymus	Thymus
18	chr12:121338800-121340600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:121339400-121340400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:121339400-121340600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr12:121339400-121340600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:121339400-121340600	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:121339400-121341200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr12:121339600-121340400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:121339600-121340400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:121339600-121340400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:121339600-121340400	Enhancers	Brain Angular Gyrus	brain
28	chr12:121339600-121340400	Enhancers	Brain Substantia Nigra	brain
29	chr12:121339600-121340400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr12:121339600-121340400	Enhancers	Right Ventricle	heart
31	chr12:121339600-121340400	Enhancers	HepG2	liver
32	chr12:121339600-121340600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:121339600-121340600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr12:121339600-121340600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr12:121339800-121340400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:121339800-121340400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:121339800-121340400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:121339800-121340400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:121339800-121340400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:121339800-121340400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:121339800-121340400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:121339800-121340400	Enhancers	Liver	Liver
43	chr12:121339800-121340400	Enhancers	Left Ventricle	heart
44	chr12:121339800-121340400	Enhancers	Psoas Muscle	Psoas
45	chr12:121339800-121340400	Active TSS	Right Atrium	heart
46	chr12:121339800-121340400	Enhancers	A549	lung
47	chr12:121339800-121340400	Enhancers	HSMMtube	muscle
48	chr12:121339800-121340600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:121339800-121340600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:121339800-121340600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links