Variant report

Variant	rs12493927
Chromosome Location	chr3:121378927-121378928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:121378460-121380063	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:121378892-121380528	Raji	blood:	n/a	n/a
3	POLR2A	chr3:121378769-121380414	GM12891	blood:	n/a	n/a
4	STAT1	chr3:121378909-121379831	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:121378647-121380088	GM12892	blood:	n/a	n/a
6	MAFK	chr3:121378918-121379232	HepG2	liver:	n/a	chr3:121379065-121379076 chr3:121379065-121379076 chr3:121379063-121379077 chr3:121379060-121379075
7	STAT5A	chr3:121378879-121380125	GM12878	blood:	n/a	n/a
8	PML	chr3:121378919-121379962	GM12878	blood:	n/a	chr3:121379202-121379210
9	NFATC1	chr3:121378755-121380352	GM12878	blood:	n/a	chr3:121379083-121379097
10	WRNIP1	chr3:121378160-121380048	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:121378663-121379973	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:121378409-121380015	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:121378844-121382265	K562	blood:	n/a	n/a
14	POLR2A	chr3:121378799-121379010	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:121378678-121379946	GM15510	blood:	n/a	n/a
16	POLR2A	chr3:121378045-121380888	GM12878	blood:	n/a	n/a
17	NFATC1	chr3:121378657-121380660	GM12878	blood:	n/a	chr3:121379083-121379097
18	CHD1	chr3:121378843-121380022	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:121376697-121380815	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:121378856-121380005	GM18526	blood:	n/a	n/a
21	RELA	chr3:121378565-121380440	GM18505	blood:	n/a	n/a
22	POLR2A	chr3:121378837-121381282	Hela-S3	cervix:	n/a	n/a
23	PML	chr3:121378506-121380475	GM12878	blood:	n/a	chr3:121379202-121379210
24	POLR2A	chr3:121377924-121380942	GM12878	blood:	n/a	n/a
25	STAT3	chr3:121378863-121380149	GM12878	blood:	n/a	chr3:121380118-121380126
26	POLR2A	chr3:121377943-121380122	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:121378738-121380069	GM19193	blood:	n/a	n/a
28	POLR2A	chr3:121378109-121380470	GM18505	blood:	n/a	n/a
29	NFIC	chr3:121378727-121380182	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:121378774-121380137	GM12892	blood:	n/a	n/a
31	POLR2A	chr3:121378446-121381026	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:121378804-121379010	GM12878	blood:	n/a	n/a
33	MXI1	chr3:121378846-121380181	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr3:121378926-121380137	GM12878	blood:	n/a	n/a
35	MTA3	chr3:121378465-121380815	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:121377978-121380138	GM12892	blood:	n/a	n/a
37	POLR2A	chr3:121378371-121380023	GM12891	blood:	n/a	n/a
38	POLR2A	chr3:121377905-121380414	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:121378598-121379935	GM18951	blood:	n/a	n/a
40	POLR2A	chr3:121378366-121380433	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121377179..121379153-chr3:121573085..121574882,2	MCF-7	breast:

Variant related genes	Relation type
RNU4-62P	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10511407	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10934556	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10934557	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934561	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs11915822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486456	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs12488717	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12489110	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489196	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489686	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap]
rs12491109	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap]
rs12491671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491714	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12492214	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12492861	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12629720	1.00[CEU][hapmap]
rs12631803	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12636562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12637265	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574654	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1814668	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919553	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1919554	1.00[JPT][hapmap]
rs1919556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971281	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2055034	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35674179	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35825165	0.87[EUR][1000 genomes]
rs3805125	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3805129	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs3966063	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4048693	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41271407	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4610269	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs55930520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55964762	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56109033	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56286202	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6762575	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6766737	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775634	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786605	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6793556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798575	0.91[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7640859	0.81[CEU][hapmap]
rs7643293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9834185	1.00[CEU][hapmap]

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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers 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	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12493927	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
2	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
3	chr3:121351400-121381400	Weak transcription	Gastric	stomach
4	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:121356800-121379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:121362200-121379400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:121362600-121379600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:121367400-121379000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:121367400-121381800	Weak transcription	Pancreas	Pancrea
10	chr3:121368800-121380000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:121370600-121379400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:121370600-121381600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
14	chr3:121372600-121379000	Weak transcription	Fetal Heart	heart
15	chr3:121373000-121380400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:121374000-121379600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:121374800-121380000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:121376400-121382200	Weak transcription	A549	lung
19	chr3:121376400-121383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:121377000-121383600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:121377200-121379200	Weak transcription	Esophagus	oesophagus
22	chr3:121377400-121379400	Enhancers	Lung	lung
23	chr3:121377400-121380800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr3:121377600-121379200	Enhancers	Left Ventricle	heart
25	chr3:121377600-121379200	Enhancers	Spleen	Spleen
26	chr3:121377600-121379400	Transcr. at gene 5' and 3'	Dnd41	blood
27	chr3:121377600-121379600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:121377800-121379400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:121377800-121379400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:121377800-121381600	Weak transcription	Fetal Brain Female	brain
31	chr3:121378000-121379000	Enhancers	Fetal Muscle Leg	muscle
32	chr3:121378000-121379000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:121378000-121379200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:121378000-121379200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr3:121378000-121379200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr3:121378000-121379200	Enhancers	Right Ventricle	heart
37	chr3:121378000-121380000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:121378000-121380400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:121378000-121388400	Strong transcription	Fetal Stomach	stomach
40	chr3:121378200-121379000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:121378200-121379200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
42	chr3:121378200-121379200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr3:121378200-121379200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr3:121378200-121379400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:121378200-121379800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr3:121378200-121379800	Active TSS	Brain Anterior Caudate	brain
47	chr3:121378200-121379800	Active TSS	Brain Hippocampus Middle	brain
48	chr3:121378200-121379800	Active TSS	Colonic Mucosa	Colon
49	chr3:121378200-121379800	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:121378200-121380000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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