Variant report

Variant	rs1861303
Chromosome Location	chr2:40896385-40896386
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10048831	0.97[ASN][1000 genomes]
rs10204982	0.84[EUR][1000 genomes]
rs10490260	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10490261	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1107932	0.86[EUR][1000 genomes]
rs11885458	0.81[AFR][1000 genomes]
rs12105490	0.84[EUR][1000 genomes]
rs12466428	0.86[EUR][1000 genomes]
rs12466571	0.83[EUR][1000 genomes]
rs12469284	0.85[EUR][1000 genomes]
rs12469295	0.86[EUR][1000 genomes]
rs12474457	0.94[EUR][1000 genomes]
rs12474560	0.94[EUR][1000 genomes]
rs12712708	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs13414829	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs17026478	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026493	0.97[ASN][1000 genomes]
rs17026498	0.97[ASN][1000 genomes]
rs17039019	0.96[ASN][1000 genomes]
rs1861302	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024437	0.82[CHD][hapmap]
rs2110791	0.82[EUR][1000 genomes]
rs2192816	0.83[EUR][1000 genomes]
rs2192819	0.85[EUR][1000 genomes]
rs2192820	0.86[EUR][1000 genomes]
rs28418485	0.80[EUR][1000 genomes]
rs34359856	0.94[EUR][1000 genomes]
rs3851317	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs3862989	0.83[EUR][1000 genomes]
rs4384832	0.83[EUR][1000 genomes]
rs4952640	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55670471	0.81[EUR][1000 genomes]
rs55690670	0.93[EUR][1000 genomes]
rs55772101	0.94[EUR][1000 genomes]
rs55814013	0.82[EUR][1000 genomes]
rs55878022	0.93[EUR][1000 genomes]
rs56121667	0.92[EUR][1000 genomes]
rs56321003	0.81[EUR][1000 genomes]
rs56336113	0.94[EUR][1000 genomes]
rs57243979	0.95[ASN][1000 genomes]
rs57625048	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60819615	0.83[EUR][1000 genomes]
rs62139487	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62139540	0.85[EUR][1000 genomes]
rs62139545	0.83[EUR][1000 genomes]
rs62139546	0.83[EUR][1000 genomes]
rs62141367	0.83[EUR][1000 genomes]
rs62141371	0.80[EUR][1000 genomes]
rs62141372	0.82[EUR][1000 genomes]
rs6708921	0.82[EUR][1000 genomes]
rs6712874	0.83[EUR][1000 genomes]
rs6720960	0.94[EUR][1000 genomes]
rs6721900	0.97[ASN][1000 genomes]
rs6733936	0.82[EUR][1000 genomes]
rs6734048	0.82[EUR][1000 genomes]
rs7563807	0.92[ASN][1000 genomes]
rs7584710	0.92[EUR][1000 genomes]
rs881189	0.85[EUR][1000 genomes]
rs888021	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv470454	chr2:40815238-40896385	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv456429	chr2:40823026-40896385	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv581507	chr2:40823026-40896385	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873924	chr2:40835285-40926138	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv581513	chr2:40843613-40896385	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
16	nsv873931	chr2:40869165-40966719	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv873932	chr2:40880043-40912597	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
18	nsv456441	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv581514	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv456452	chr2:40890416-40989061	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv581515	chr2:40890416-40989061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1861303	TMEM178	cis	parietal	SCAN
rs1861303	FEZ2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40893600-40896400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:40895000-40896800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:40895000-40896800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:40895200-40896400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:40895400-40896400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr2:40895400-40896800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:40895400-40896800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:40895600-40896400	Weak transcription	Fetal Kidney	kidney
9	chr2:40895600-40896600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:40895600-40896800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:40895600-40896800	Enhancers	Dnd41	blood
12	chr2:40896000-40896600	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr2:40896200-40896400	Enhancers	Pancreas	Pancrea
14	chr2:40896200-40896600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:40896200-40896600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast

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