Variant report

Variant	rs12463554
Chromosome Location	chr2:148751612-148751613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1014064	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1015096	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs10186643	0.86[EUR][1000 genomes]
rs10460259	1.00[CEU][hapmap]
rs10497024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10497026	0.88[ASN][1000 genomes]
rs10497029	0.81[ASN][1000 genomes]
rs10803523	0.96[CEU][hapmap]
rs1128919	1.00[CEU][hapmap]
rs11886876	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11888152	1.00[CEU][hapmap]
rs11896010	0.98[EUR][1000 genomes]
rs11900506	0.88[CEU][hapmap]
rs11901963	0.96[CEU][hapmap]
rs12053401	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs12105411	0.80[EUR][1000 genomes]
rs12463798	0.96[CEU][hapmap]
rs12465610	0.82[AFR][1000 genomes]
rs12467336	0.82[AFR][1000 genomes]
rs12469015	0.89[ASN][1000 genomes]
rs12469509	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12469939	0.89[ASN][1000 genomes]
rs12472459	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12473564	0.83[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12476827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12691776	0.84[ASN][1000 genomes]
rs12987286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12989250	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12990959	0.88[CEU][hapmap]
rs12992412	0.88[CEU][hapmap]
rs12997165	0.97[EUR][1000 genomes]
rs12998729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13001158	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13003171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004041	0.89[ASN][1000 genomes]
rs13006184	0.84[ASN][1000 genomes]
rs13006721	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13007770	0.97[EUR][1000 genomes]
rs13008497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs13008838	0.98[EUR][1000 genomes]
rs13012455	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13013887	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13014936	0.98[EUR][1000 genomes]
rs13015552	0.88[ASN][1000 genomes]
rs13019809	0.96[CEU][hapmap]
rs13021605	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13022962	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs13026650	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs13027200	0.88[ASN][1000 genomes]
rs13027706	1.00[CEU][hapmap]
rs13028348	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs13029038	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13029714	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13032303	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13032786	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13032810	0.98[EUR][1000 genomes]
rs13033664	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13033696	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs13035475	0.98[EUR][1000 genomes]
rs1364658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1424944	1.00[CEU][hapmap]
rs1424954	1.00[CEU][hapmap]
rs1469210	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs1531032	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1598207	0.92[CEU][hapmap];0.99[EUR][1000 genomes]
rs16828270	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16828354	0.86[AFR][1000 genomes]
rs1863152	0.88[CEU][hapmap]
rs1863153	0.88[CEU][hapmap]
rs1975748	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs1991169	0.88[CEU][hapmap]
rs2113793	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs2122386	0.88[ASN][1000 genomes]
rs2161983	0.96[CEU][hapmap]
rs2161984	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs2168145	0.96[EUR][1000 genomes]
rs2288190	0.84[CEU][hapmap]
rs2303392	0.96[CEU][hapmap]
rs2307394	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs2382201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2382211	0.80[ASN][1000 genomes]
rs2890915	0.98[EUR][1000 genomes]
rs3764955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs3768687	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs3768689	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs4417662	0.97[EUR][1000 genomes]
rs4972320	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4972321	0.97[EUR][1000 genomes]
rs4972332	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6430281	0.98[EUR][1000 genomes]
rs6430282	0.98[EUR][1000 genomes]
rs6711673	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs6724719	0.99[EUR][1000 genomes]
rs6729804	0.88[EUR][1000 genomes]
rs6729997	0.81[ASN][1000 genomes]
rs6732463	0.99[EUR][1000 genomes]
rs6734998	0.88[CEU][hapmap]
rs6746415	0.98[EUR][1000 genomes]
rs71350069	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs72855232	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7425436	0.93[EUR][1000 genomes]
rs7560425	0.98[EUR][1000 genomes]
rs7568811	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7574180	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7580733	0.82[AFR][1000 genomes]
rs7583759	0.88[ASN][1000 genomes]
rs7595286	0.81[ASN][1000 genomes]
rs7598361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs897172	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs929939	0.92[CEU][hapmap]
rs9789434	0.95[EUR][1000 genomes]
rs9789640	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1004169	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv535970	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv869326	chr2:148727068-148859804	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1009807	chr2:148731025-148829378	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv535973	chr2:148731025-148829378	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv1009696	chr2:148739650-148805668	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv535974	chr2:148739650-148805668	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv1011381	chr2:148739850-148805529	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv535975	chr2:148739850-148805529	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv999777	chr2:148740742-148809464	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
24	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv1015003	chr2:148745734-148839653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148694200-148777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:148709400-148776800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:148721400-148752800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:148721400-148763600	Weak transcription	Spleen	Spleen
6	chr2:148722800-148756400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:148726400-148752600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:148726600-148752600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:148728200-148773400	Weak transcription	K562	blood
10	chr2:148730800-148752600	Weak transcription	Primary T cells from cord blood	blood
11	chr2:148731400-148752800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:148736000-148776800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:148736200-148752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:148736200-148752400	Weak transcription	Fetal Intestine Small	intestine
15	chr2:148736200-148752600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:148736200-148752800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:148736400-148765600	Weak transcription	A549	lung
18	chr2:148736600-148752600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:148736600-148752600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:148737000-148753200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:148737600-148752600	Weak transcription	Primary B cells from cord blood	blood
22	chr2:148737600-148752600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:148739000-148752600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:148739000-148759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:148741200-148758000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:148741600-148755800	Weak transcription	Ovary	ovary
27	chr2:148741600-148756200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:148741800-148752800	Weak transcription	Thymus	Thymus
29	chr2:148741800-148757400	Weak transcription	Aorta	Aorta
30	chr2:148742200-148755800	Weak transcription	Gastric	stomach
31	chr2:148742400-148755800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:148742400-148756000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:148742800-148752800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:148743600-148757800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:148743600-148757800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:148744400-148754200	Weak transcription	HepG2	liver
37	chr2:148744600-148755800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:148746200-148752600	Weak transcription	Lung	lung
39	chr2:148747400-148752600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:148747400-148752800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:148747400-148758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:148747800-148752600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:148748000-148752600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:148748000-148752800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:148748000-148752800	Weak transcription	Fetal Lung	lung
46	chr2:148748000-148752800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:148748000-148753200	Weak transcription	Placenta	Placenta
48	chr2:148748000-148754200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:148748000-148771400	Weak transcription	Fetal Kidney	kidney
50	chr2:148748200-148752000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links