Variant report

Variant	rs13254996
Chromosome Location	chr8:87194368-87194369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87193443..87195770-chr8:87354919..87356635,3	MCF-7	breast:
2	chr8:87192734..87196437-chr8:87354857..87357737,4	MCF-7	breast:
3	chr8:87193009..87195641-chr8:87198363..87201280,2	MCF-7	breast:
4	chr8:87187644..87190858-chr8:87193352..87196070,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254231	Chromatin interaction
ENSG00000123124	Chromatin interaction

Extended variants
information (count: 197 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10091781	0.82[ASN][1000 genomes]
rs10097379	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10098631	0.82[JPT][hapmap]
rs10098643	0.83[ASN][1000 genomes]
rs10099368	0.82[JPT][hapmap]
rs10102252	0.86[JPT][hapmap]
rs10103166	0.86[JPT][hapmap]
rs10106391	0.82[JPT][hapmap]
rs10106497	0.86[JPT][hapmap]
rs10108391	0.82[ASN][1000 genomes]
rs10111656	0.82[ASN][1000 genomes]
rs10112076	0.82[JPT][hapmap]
rs10112474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10504819	0.81[JPT][hapmap]
rs10956188	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10956207	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10956310	0.93[ASN][1000 genomes]
rs11777902	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787431	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11988449	0.81[JPT][hapmap]
rs12115123	0.91[ASN][1000 genomes]
rs12155639	0.84[ASN][1000 genomes]
rs12155804	0.86[ASN][1000 genomes]
rs12155824	0.87[ASN][1000 genomes]
rs12155882	0.88[ASN][1000 genomes]
rs12156219	0.89[ASN][1000 genomes]
rs12541053	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12541292	0.93[ASN][1000 genomes]
rs12541468	0.93[ASN][1000 genomes]
rs12541480	0.93[ASN][1000 genomes]
rs12541499	0.93[ASN][1000 genomes]
rs12541961	0.87[ASN][1000 genomes]
rs12544098	0.93[ASN][1000 genomes]
rs12546120	0.93[ASN][1000 genomes]
rs12546618	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12548440	0.93[ASN][1000 genomes]
rs13257877	0.86[JPT][hapmap]
rs13259716	0.93[ASN][1000 genomes]
rs13262822	0.87[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13265507	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs13267067	0.82[JPT][hapmap]
rs13267165	0.93[ASN][1000 genomes]
rs13267261	0.92[ASN][1000 genomes]
rs13268911	0.91[ASN][1000 genomes]
rs13272356	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13272593	0.93[ASN][1000 genomes]
rs13276090	0.86[ASN][1000 genomes]
rs13276129	0.86[ASN][1000 genomes]
rs13280528	0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13281890	0.86[JPT][hapmap]
rs13282492	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1384878	0.81[JPT][hapmap]
rs1384879	0.81[JPT][hapmap]
rs16887456	0.82[JPT][hapmap]
rs2318396	0.82[JPT][hapmap]
rs2626333	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2626337	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2626338	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2626341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2626343	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2721248	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2721252	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2721255	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2976187	0.84[CHD][hapmap]
rs2976190	0.84[CHD][hapmap]
rs33979484	0.86[ASN][1000 genomes]
rs34122951	0.89[ASN][1000 genomes]
rs34522097	0.93[ASN][1000 genomes]
rs34660447	0.93[ASN][1000 genomes]
rs34683419	0.91[ASN][1000 genomes]
rs34733066	0.91[ASN][1000 genomes]
rs34744391	0.93[ASN][1000 genomes]
rs34844115	0.81[ASN][1000 genomes]
rs34847457	0.91[ASN][1000 genomes]
rs35141817	0.93[ASN][1000 genomes]
rs35174822	0.93[ASN][1000 genomes]
rs35292130	0.91[ASN][1000 genomes]
rs35330967	0.89[ASN][1000 genomes]
rs35332272	0.90[ASN][1000 genomes]
rs35715881	0.93[ASN][1000 genomes]
rs35844270	0.93[ASN][1000 genomes]
rs35978872	0.90[ASN][1000 genomes]
rs3923638	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4076880	0.93[ASN][1000 genomes]
rs4076881	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4311641	0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4319071	0.86[ASN][1000 genomes]
rs4355748	0.91[ASN][1000 genomes]
rs4443642	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4480105	0.83[ASN][1000 genomes]
rs4515529	0.93[ASN][1000 genomes]
rs4571715	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4581031	0.86[ASN][1000 genomes]
rs4596629	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596630	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4960953	0.81[JPT][hapmap]
rs4960955	0.81[JPT][hapmap]
rs4960959	0.82[JPT][hapmap]
rs4961077	0.81[JPT][hapmap]
rs4961092	0.86[JPT][hapmap]
rs58965951	0.93[ASN][1000 genomes]
rs59777373	0.92[ASN][1000 genomes]
rs6470428	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6470714	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6470732	0.86[ASN][1000 genomes]
rs6470733	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs67091588	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67149475	0.93[ASN][1000 genomes]
rs67650717	0.84[ASN][1000 genomes]
rs6981788	0.88[ASN][1000 genomes]
rs6982731	0.91[ASN][1000 genomes]
rs6986074	0.85[ASN][1000 genomes]
rs6990582	0.83[ASN][1000 genomes]
rs6990782	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6991607	0.88[ASN][1000 genomes]
rs6993377	0.81[JPT][hapmap]
rs6996246	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs6999252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7001524	0.87[ASN][1000 genomes]
rs7001674	0.86[JPT][hapmap]
rs7001699	0.90[JPT][hapmap]
rs7005558	0.89[ASN][1000 genomes]
rs7010778	0.99[ASN][1000 genomes]
rs7011242	0.93[ASN][1000 genomes]
rs7013212	0.88[ASN][1000 genomes]
rs7013268	0.88[ASN][1000 genomes]
rs7013552	0.87[ASN][1000 genomes]
rs7014188	0.88[ASN][1000 genomes]
rs7016268	0.86[JPT][hapmap]
rs7016450	0.83[ASN][1000 genomes]
rs7017607	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7017743	0.89[ASN][1000 genomes]
rs72606619	0.83[ASN][1000 genomes]
rs72606620	0.83[ASN][1000 genomes]
rs72606621	0.82[ASN][1000 genomes]
rs72606622	0.83[ASN][1000 genomes]
rs72606623	0.86[ASN][1000 genomes]
rs72606624	0.86[ASN][1000 genomes]
rs72606625	0.86[ASN][1000 genomes]
rs72606626	0.86[ASN][1000 genomes]
rs72606627	0.82[ASN][1000 genomes]
rs72606629	0.93[ASN][1000 genomes]
rs72606630	0.93[ASN][1000 genomes]
rs7350116	0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7461255	0.83[ASN][1000 genomes]
rs7821560	0.86[JPT][hapmap]
rs7823544	0.85[ASN][1000 genomes]
rs7825985	0.93[ASN][1000 genomes]
rs7827938	0.85[ASN][1000 genomes]
rs7836003	0.81[JPT][hapmap]
rs7837251	0.82[JPT][hapmap]
rs7846210	0.93[ASN][1000 genomes]
rs9643132	0.81[JPT][hapmap]
rs9643143	0.86[JPT][hapmap]
rs9969464	0.85[ASN][1000 genomes]
rs9969498	0.84[ASN][1000 genomes]
rs9969499	0.84[ASN][1000 genomes]
rs9969529	0.85[ASN][1000 genomes]
rs9969581	0.83[ASN][1000 genomes]
rs9969582	0.84[ASN][1000 genomes]
rs9969612	0.83[ASN][1000 genomes]
rs9969617	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428204	chr8:86405478-87312208	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv891147	chr8:86886950-87333968	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv611674	chr8:87156172-87315920	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1027648	chr8:87161437-87319476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv429926	chr8:87161695-87429872	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1815028	chr8:87166396-87205568	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1020485	chr8:87167184-87330873	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1023114	chr8:87167184-87335197	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1033960	chr8:87167790-87334194	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1016050	chr8:87167790-87335197	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv6290	chr8:87175740-87229808	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1016177	chr8:87177368-87319476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1023772	chr8:87177368-87334194	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1031874	chr8:87177368-87335197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1030401	chr8:87177368-87337260	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1033007	chr8:87185458-87319476	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	esv2761445	chr8:87185470-87335197	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	esv1810589	chr8:87187050-87201127	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	esv1811895	chr8:87187050-87201127	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv465733	chr8:87187050-87302328	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv611675	chr8:87187050-87302328	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv519507	chr8:87187195-87333968	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
26	esv18804	chr8:87188259-87195171	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	esv1812977	chr8:87188805-87201127	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv611683	chr8:87188805-87201127	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	esv1810583	chr8:87188869-87199505	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	esv1804344	chr8:87188869-87205885	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
31	esv1805667	chr8:87188869-87205885	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	esv1810186	chr8:87188869-87205885	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
33	esv1811924	chr8:87188869-87205885	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
34	esv3481065	chr8:87190036-87195234	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
35	esv3481066	chr8:87190036-87195234	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13254996	CPNE3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87192600-87194600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:87192600-87195000	Enhancers	NHEK	skin
3	chr8:87192800-87195000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr8:87193000-87194400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:87194000-87194400	Enhancers	HMEC	breast
6	chr8:87194000-87194600	Weak transcription	Fetal Lung	lung
7	chr8:87194200-87194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr8:87194200-87194600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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