Variant report

Variant	rs1034405
Chromosome Location	chr3:50597092-50597093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:50595775..50597292-chr3:50644098..50646592,2	MCF-7	breast:
2	chr3:50597009..50601269-chr3:50602729..50605113,3	K562	blood:
3	chr3:50596509..50599002-chr3:50637858..50640256,2	MCF-7	breast:
4	chr3:50594685..50598509-chr3:50599030..50605276,6	K562	blood:
5	chr3:50597015..50599006-chr3:50606091..50608071,2	MCF-7	breast:
6	chr3:50595096..50597845-chr3:50598806..50601050,2	MCF-7	breast:
7	chr3:50593179..50595376-chr3:50596948..50598840,3	MCF-7	breast:
8	chr3:50587657..50590560-chr3:50595008..50597465,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs11130252	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130255	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11710858	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11719998	0.85[EUR][1000 genomes]
rs12491425	0.86[EUR][1000 genomes]
rs12639126	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs129310	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs13076850	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083004	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084476	0.93[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094785	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13095920	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs13096264	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1385025	0.89[YRI][hapmap]
rs1458386	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs1458387	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1463496	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1463497	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs175634	0.94[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17787569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824280	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs201193	0.86[EUR][1000 genomes]
rs201194	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs201196	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201197	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125366	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2125369	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2168866	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs2227280	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232248	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2232253	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269505	1.00[CEU][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs2269507	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355321	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355323	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs2608988	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2609036	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2675810	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2883652	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs34202063	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34267788	0.89[EUR][1000 genomes]
rs34399912	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34434811	0.89[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756253	0.93[EUR][1000 genomes]
rs34762184	0.89[CHD][hapmap]
rs34889917	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35655236	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35690191	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714264	0.94[EUR][1000 genomes]
rs35864641	0.89[EUR][1000 genomes]
rs375544	0.86[TSI][hapmap];0.93[YRI][hapmap]
rs3792325	0.93[YRI][hapmap]
rs3792328	0.86[TSI][hapmap];0.93[YRI][hapmap]
rs3804627	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs3804628	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs388483	0.83[YRI][hapmap]
rs391620	0.85[EUR][1000 genomes]
rs396302	0.86[TSI][hapmap];0.89[YRI][hapmap]
rs398703	0.86[EUR][1000 genomes]
rs399484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399971	0.89[EUR][1000 genomes]
rs414171	0.81[EUR][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs441516	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs4429624	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs443030	0.90[EUR][1000 genomes]
rs443436	0.89[YRI][hapmap]
rs448028	0.89[YRI][hapmap]
rs4533647	0.89[EUR][1000 genomes]
rs453570	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs4688702	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs490634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59949730	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609678	0.81[AFR][1000 genomes]
rs616589	0.93[YRI][hapmap]
rs622502	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs628081	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6446212	0.93[YRI][hapmap]
rs6446214	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs667894	0.87[LWK][hapmap];0.86[MKK][hapmap]
rs67425923	0.84[EUR][1000 genomes]
rs67588094	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768300	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6775012	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6778680	0.82[CEU][hapmap]
rs6779819	0.86[TSI][hapmap]
rs67813889	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784166	0.94[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791880	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs6796769	0.86[TSI][hapmap]
rs695170	0.91[EUR][1000 genomes]
rs71326937	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728901	0.93[YRI][hapmap]
rs73082948	0.87[EUR][1000 genomes]
rs750453	0.85[EUR][1000 genomes]
rs750510	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs7611428	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs7615703	0.86[TSI][hapmap]
rs7629253	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7646236	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs7650574	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7652260	0.82[EUR][1000 genomes]
rs7652715	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs809451	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs809454	0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs813243	0.86[TSI][hapmap];0.89[YRI][hapmap]
rs900735	0.89[YRI][hapmap]
rs936405	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs936406	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs9682401	0.89[YRI][hapmap]
rs9830920	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9839684	1.00[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1034405	CAMP	cis	cerebellum	SCAN
rs1034405	APEH	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50583600-50603400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:50586000-50597200	Weak transcription	Right Atrium	heart
3	chr3:50587600-50603800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:50588400-50603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:50589600-50604000	Weak transcription	Fetal Lung	lung
6	chr3:50592600-50597200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:50592800-50604000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:50593400-50601400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:50593400-50602800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:50593600-50604000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:50593800-50604200	Weak transcription	Brain Germinal Matrix	brain
12	chr3:50594200-50604000	Weak transcription	Pancreas	Pancrea
13	chr3:50594600-50597400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:50594600-50604000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:50594800-50601000	Weak transcription	Fetal Brain Female	brain
16	chr3:50594800-50604000	Weak transcription	Adipose Nuclei	Adipose
17	chr3:50595600-50604000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:50595800-50599000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:50595800-50600000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:50595800-50603200	Strong transcription	Fetal Stomach	stomach
21	chr3:50595800-50604200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:50595800-50604400	Weak transcription	Primary T cells from cord blood	blood
23	chr3:50596000-50598400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:50596200-50597400	Strong transcription	Fetal Intestine Small	intestine
25	chr3:50596200-50598200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:50596200-50604200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:50596400-50597200	Weak transcription	Spleen	Spleen
28	chr3:50596400-50599000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr3:50596400-50603800	Weak transcription	Fetal Heart	heart
30	chr3:50596600-50598800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:50596600-50598800	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:50596600-50604000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:50596800-50597600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:50596800-50597600	Enhancers	Gastric	stomach
35	chr3:50596800-50597800	Enhancers	Right Ventricle	heart
36	chr3:50596800-50603200	Weak transcription	Brain Angular Gyrus	brain
37	chr3:50597000-50597600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:50597000-50597600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:50597000-50597800	Enhancers	Left Ventricle	heart
40	chr3:50597000-50597800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:50597000-50597800	Enhancers	NHDF-Ad	bronchial
42	chr3:50597000-50603000	Weak transcription	Ovary	ovary
43	chr3:50597000-50603800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:50597000-50604000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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