Variant report

Variant	rs13746
Chromosome Location	chr12:121201167-121201168
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	chr12:121199470..121201795-chr12:121202855..121205373,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1027556	0.83[YRI][hapmap]
rs1039302	0.83[YRI][hapmap]
rs10431387	0.83[YRI][hapmap]
rs10437838	0.83[YRI][hapmap]
rs10774569	0.83[YRI][hapmap]
rs10774571	0.83[YRI][hapmap]
rs10774572	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10849786	0.81[YRI][hapmap]
rs10849791	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849807	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10849810	0.83[YRI][hapmap]
rs10849811	0.83[YRI][hapmap]
rs11065259	0.83[YRI][hapmap]
rs11065264	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065282	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11065283	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11065292	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11065298	0.83[YRI][hapmap]
rs11065300	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11065311	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11065322	0.83[YRI][hapmap]
rs11065324	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1151849	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs1151862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11611087	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs1177585	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12579868	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580949	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs12822123	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1467283	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1542859	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1696357	0.81[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs1718180	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2015462	0.94[ASN][1000 genomes]
rs2047568	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs2393717	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2393718	0.81[YRI][hapmap]
rs2461475	0.80[EUR][1000 genomes]
rs2893876	0.85[ASN][1000 genomes]
rs3213566	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3213567	0.94[ASN][1000 genomes]
rs3213568	0.83[YRI][hapmap]
rs3213570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213571	0.83[YRI][hapmap]
rs3213572	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809313	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3809314	0.83[YRI][hapmap]
rs3842985	0.82[ASN][1000 genomes]
rs3861797	0.82[ASN][1000 genomes]
rs3883901	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs3897746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs3901854	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4454799	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs471688	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4767937	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487943	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs494632	0.86[EUR][1000 genomes]
rs508595	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520753	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs525425	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531782	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs533264	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs534415	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs548452	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs572016	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs577961	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs580240	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590625	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs602984	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs608394	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609700	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs610694	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs618482	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs624216	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs625228	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.90[YRI][hapmap]
rs647881	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6489780	0.83[YRI][hapmap]
rs661647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs665585	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs668622	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7135147	0.83[YRI][hapmap]
rs7137504	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7139145	0.83[YRI][hapmap]
rs715319	0.83[YRI][hapmap]
rs7298639	0.83[YRI][hapmap]
rs7305849	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7965332	0.83[YRI][hapmap]
rs869781	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs909053	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9431	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989986	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]

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	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13746	HPD	cis	parietal	SCAN
rs13746	SRRM4	cis	cerebellum	SCAN
rs13746	P2RX4	cis	cerebellum	SCAN
rs13746	WSB2	cis	cerebellum	SCAN
rs13746	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx
rs13746	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs13746	SPPL3	cis	parietal	SCAN
rs13746	SPPL3	cis	cerebellum	SCAN
rs13746	UNQ1887	cis	Temporal Cortex	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121194200-121202200	Weak transcription	K562	blood
2	chr12:121195000-121201200	Weak transcription	Small Intestine	intestine
3	chr12:121195600-121204200	Weak transcription	Stomach Mucosa	stomach
4	chr12:121195600-121207200	Strong transcription	Brain Germinal Matrix	brain
5	chr12:121196400-121207000	Strong transcription	Fetal Brain Female	brain
6	chr12:121196800-121201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:121196800-121203000	Strong transcription	Fetal Intestine Large	intestine
8	chr12:121196800-121212800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:121197000-121203000	Strong transcription	Fetal Intestine Small	intestine
10	chr12:121197000-121207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:121197200-121201200	Weak transcription	Ovary	ovary
12	chr12:121197200-121204200	Weak transcription	Fetal Brain Male	brain
13	chr12:121197200-121210000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:121197400-121201200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:121197400-121203000	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr12:121197400-121203400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:121197400-121203400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:121197400-121203800	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:121197400-121207000	Strong transcription	Pancreas	Pancrea
20	chr12:121197400-121209800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:121197400-121212600	Strong transcription	Thymus	Thymus
22	chr12:121197400-121220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:121197600-121203000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr12:121197600-121204400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:121197600-121205400	Strong transcription	GM12878-XiMat	blood
26	chr12:121197600-121207200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:121197600-121210400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:121197800-121203400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:121197800-121209000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:121197800-121212400	Strong transcription	Liver	Liver
31	chr12:121197800-121220400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:121198000-121201200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:121198000-121201400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:121198000-121202600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:121198000-121207200	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr12:121198000-121207200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:121198000-121212000	Strong transcription	Adipose Nuclei	Adipose
38	chr12:121198200-121201400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:121198200-121201600	Genic enhancers	Placenta	Placenta
40	chr12:121198200-121203800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:121198200-121204200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:121198200-121205600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr12:121198200-121211400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:121198400-121207200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:121198400-121209800	Strong transcription	Dnd41	blood
46	chr12:121198400-121212200	Strong transcription	Primary B cells from cord blood	blood
47	chr12:121198400-121220800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:121198600-121203000	Strong transcription	Colonic Mucosa	Colon
49	chr12:121198600-121209200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:121198800-121201600	Genic enhancers	Brain Hippocampus Middle	brain

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