Variant report

Variant	rs34405399
Chromosome Location	chr10:981015-981016
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	MAX	chr10:980532-981462	HepG2	liver:	n/a	chr10:980795-980806
2	MAX	chr10:980635-981453	HepG2	liver:	n/a	chr10:980795-980806
3	HNF4G	chr10:980792-981322	HepG2	liver:	n/a	chr10:980943-980951 chr10:980937-980952 chr10:980935-980953 chr10:980938-980950 chr10:980937-980952 chr10:980937-980952 chr10:981162-981176 chr10:981162-981177
4	HNF4A	chr10:980706-981015	HepG2	liver:	n/a	chr10:980943-980951 chr10:980937-980952 chr10:980935-980953 chr10:980938-980950 chr10:980937-980952 chr10:980937-980952 chr10:980936-980951
5	HNF4A	chr10:980747-981290	HepG2	liver:	n/a	chr10:980943-980951 chr10:980937-980952 chr10:980935-980953 chr10:980938-980950 chr10:980937-980952 chr10:980937-980952 chr10:981162-981176 chr10:981162-981177 chr10:980936-980951
6	POLR2A	chr10:980713-981409	HepG2	liver:	n/a	n/a
7	HNF4G	chr10:980807-981299	HepG2	liver:	n/a	chr10:980943-980951 chr10:980937-980952 chr10:980935-980953 chr10:980938-980950 chr10:980937-980952 chr10:980937-980952 chr10:981162-981176 chr10:981162-981177
8	EP300	chr10:980707-981276	HepG2	liver:	n/a	n/a
9	POLR2A	chr10:980976-981332	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr10:980700-981194	HepG2	liver:	n/a	n/a
11	HEY1	chr10:980871-981305	HepG2	liver:	n/a	n/a
12	MYC	chr10:980800-981036	HepG2	liver:	n/a	n/a
13	POLR2A	chr10:980876-981043	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:980826..983608-chr10:1003068..1004956,2	K562	blood:
2	chr10:979434..982350-chr10:995576..997645,2	MCF-7	breast:
3	chr10:980753..982426-chr17:57919026..57921181,2	MCF-7	breast:
4	chr10:980642..983775-chr10:1008969..1010804,3	K562	blood:

Variant related genes	Relation type
LARP4B	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1013505	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs10508208	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs10904577	1.00[ASN][1000 genomes]
rs10904580	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904581	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904584	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106064	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253444	0.89[CEU][hapmap]
rs11253445	0.89[CEU][hapmap]
rs11253446	0.89[CEU][hapmap]
rs11253458	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253459	0.88[CEU][hapmap]
rs11253460	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253465	1.00[ASN][1000 genomes]
rs11253467	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11253468	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253473	1.00[ASN][1000 genomes]
rs11253475	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253485	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253488	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253492	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253493	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253494	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11253495	0.94[CEU][hapmap];0.82[YRI][hapmap]
rs11253499	1.00[ASN][1000 genomes]
rs11253504	0.88[CEU][hapmap]
rs11253509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253511	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253513	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253517	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253520	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253521	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812170	1.00[ASN][1000 genomes]
rs11812523	1.00[ASN][1000 genomes]
rs11813210	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11815185	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11816064	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11817793	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11818288	1.00[ASN][1000 genomes]
rs11818325	1.00[ASN][1000 genomes]
rs12240651	1.00[ASN][1000 genomes]
rs12244253	1.00[ASN][1000 genomes]
rs12244355	1.00[ASN][1000 genomes]
rs12249634	1.00[ASN][1000 genomes]
rs12249828	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs12250936	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12250937	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12251396	1.00[ASN][1000 genomes]
rs12254002	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs12258388	1.00[ASN][1000 genomes]
rs12259338	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259720	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12260800	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs12261911	1.00[ASN][1000 genomes]
rs12264390	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264711	1.00[ASN][1000 genomes]
rs12267709	1.00[ASN][1000 genomes]
rs12354639	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357633	0.89[CEU][hapmap]
rs12359645	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360270	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12762973	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12763396	0.94[CEU][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs12764024	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs12765174	1.00[ASN][1000 genomes]
rs12766381	1.00[ASN][1000 genomes]
rs12768348	0.89[CEU][hapmap]
rs12769002	0.89[CEU][hapmap]
rs12769431	1.00[ASN][1000 genomes]
rs12769873	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12770190	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs12774985	0.89[CEU][hapmap]
rs12778891	1.00[ASN][1000 genomes]
rs12783472	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377166	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs1341741	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs1341742	1.00[ASN][1000 genomes]
rs1539174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555899	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs17159950	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs17159970	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs2050944	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs34254874	1.00[ASN][1000 genomes]
rs34270014	1.00[ASN][1000 genomes]
rs34284130	1.00[ASN][1000 genomes]
rs34433840	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34847097	1.00[ASN][1000 genomes]
rs35174953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35394603	1.00[ASN][1000 genomes]
rs35567307	1.00[ASN][1000 genomes]
rs35637113	1.00[ASN][1000 genomes]
rs35693858	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825568	1.00[ASN][1000 genomes]
rs35968821	1.00[ASN][1000 genomes]
rs4522091	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs56318703	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56347655	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61830929	1.00[ASN][1000 genomes]
rs61830932	1.00[ASN][1000 genomes]
rs7067865	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7074642	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7077278	0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs72778229	1.00[ASN][1000 genomes]
rs765867	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7908138	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914758	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS 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 miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
11	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	nsv825207	chr10:957020-1005451	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
17	nsv825208	chr10:965883-1004836	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34405399	DIP2C	cis	cerebellum	SCAN
rs34405399	ADARB2	cis	parietal	SCAN
rs34405399	PFKP	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:978200-985000	Weak transcription	Spleen	Spleen
2	chr10:978200-985400	Weak transcription	Brain Angular Gyrus	brain
3	chr10:978400-982200	Weak transcription	Lung	lung
4	chr10:978400-982200	Weak transcription	GM12878-XiMat	blood
5	chr10:978400-982400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr10:978400-984800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:978400-985800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:979200-983200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:979200-984800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:979400-983000	Weak transcription	Placenta	Placenta
11	chr10:979400-983800	Weak transcription	Psoas Muscle	Psoas
12	chr10:979800-985000	Weak transcription	Dnd41	blood
13	chr10:980000-985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:980600-981200	Enhancers	Fetal Kidney	kidney
15	chr10:980600-981600	Flanking Active TSS	HepG2	liver
16	chr10:980800-981400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:981000-981200	Enhancers	Skeletal Muscle Male	skeletal muscle

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