Variant report

Variant	rs4443426
Chromosome Location	chr5:43279572-43279573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43278970..43281149-chr5:43285942..43288845,2	MCF-7	breast:
2	chr5:43277970..43279985-chr5:43281454..43283033,2	K562	blood:
3	chr5:43272071..43275298-chr5:43277638..43280213,3	K562	blood:
4	chr5:43276038..43279820-chr5:43312022..43314782,3	K562	blood:

Variant related genes	Relation type
ENSG00000261604	Chromatin interaction
ENSG00000112972	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10039048	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs10039617	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs10065852	0.96[CEU][hapmap]
rs10462047	0.86[EUR][1000 genomes]
rs10462048	0.92[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10512825	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10512827	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs10512828	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs10805671	0.96[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs10805672	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10805673	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805674	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805675	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs10941620	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10941621	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941622	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941623	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941628	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10941630	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10941631	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs11738086	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739009	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11739665	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740128	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741246	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741797	0.80[CHB][hapmap]
rs11742171	0.96[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11742712	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11743622	0.96[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs11743633	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs11746629	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11747105	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11747834	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11950040	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs11950448	0.96[CEU][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11951515	0.89[CHB][hapmap]
rs11951584	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11956635	0.92[CEU][hapmap]
rs11956988	0.92[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs12189016	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12189447	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12514393	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12514399	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12515072	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12516435	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12517362	0.81[EUR][1000 genomes]
rs12518032	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12518127	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs12519554	0.88[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12520012	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12522178	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13659	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1545753	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1548097	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1564196	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1564197	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1564198	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs17244818	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs2086133	0.89[EUR][1000 genomes]
rs2126948	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2126949	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2169781	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2330242	0.80[EUR][1000 genomes]
rs35231094	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35239179	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733768	0.96[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3733769	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756416	0.80[CHB][hapmap]
rs4050485	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254917	0.82[EUR][1000 genomes]
rs4288122	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4320264	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4373285	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4395639	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4443425	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4574553	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4591755	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4866734	0.88[EUR][1000 genomes]
rs4866737	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866738	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866741	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs4866813	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866818	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs4866820	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4866821	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4866822	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4866824	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4866825	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55634155	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55647314	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55759722	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55794239	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55800451	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55820064	0.82[ASN][1000 genomes]
rs55939301	0.87[ASN][1000 genomes]
rs55992392	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56023994	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56029402	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56071328	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56114604	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56185290	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56206275	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56331753	0.82[ASN][1000 genomes]
rs57066570	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57392430	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57401732	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58358642	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58679159	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58966636	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59078439	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59625262	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59814709	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60207549	0.86[EUR][1000 genomes]
rs60445501	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61627503	0.81[EUR][1000 genomes]
rs6451684	0.96[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs66585077	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66691321	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66914803	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67415672	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67497876	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67620667	0.80[EUR][1000 genomes]
rs67651757	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67817333	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6814	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863246	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6863360	0.82[EUR][1000 genomes]
rs6886499	0.88[CEU][hapmap];0.88[CHB][hapmap]
rs6887351	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6895805	0.91[EUR][1000 genomes]
rs6898398	0.82[EUR][1000 genomes]
rs7380703	0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7701391	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7704588	0.96[CEU][hapmap]
rs7708779	0.96[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7714027	0.92[CEU][hapmap]
rs7714919	0.82[EUR][1000 genomes]
rs7716091	0.96[CEU][hapmap]
rs7720165	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7720681	0.92[CEU][hapmap];0.80[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs7727047	0.89[CEU][hapmap];0.80[CHB][hapmap];0.82[TSI][hapmap]
rs7734293	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922439	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9292871	0.96[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9790987	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
4	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
5	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4443426	HMGCS1	cis	cerebellum	SCAN
rs4443426	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43246600-43281400	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:43271200-43280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:43274400-43287000	Weak transcription	Left Ventricle	heart
4	chr5:43274600-43285000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:43274600-43286800	Weak transcription	Esophagus	oesophagus
6	chr5:43274800-43286400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:43274800-43286600	Weak transcription	Stomach Mucosa	stomach
8	chr5:43275000-43286400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:43275000-43286400	Weak transcription	GM12878-XiMat	blood
10	chr5:43275000-43286600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:43275600-43286400	Weak transcription	Fetal Brain Female	brain
12	chr5:43275800-43286800	Weak transcription	Liver	Liver
13	chr5:43275800-43286800	Weak transcription	Gastric	stomach
14	chr5:43276600-43286200	Weak transcription	Brain Germinal Matrix	brain
15	chr5:43276600-43286600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:43277800-43281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:43277800-43281400	Weak transcription	K562	blood
18	chr5:43277800-43286800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:43278800-43280400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:43279000-43281600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:43279000-43282400	Weak transcription	Fetal Heart	heart
22	chr5:43279200-43280400	Enhancers	Adipose Nuclei	Adipose
23	chr5:43279200-43280600	Strong transcription	Brain Substantia Nigra	brain
24	chr5:43279400-43280200	Weak transcription	Brain Angular Gyrus	brain
25	chr5:43279400-43280600	Strong transcription	Brain Cingulate Gyrus	brain
26	chr5:43279400-43282600	Strong transcription	Brain Anterior Caudate	brain

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