Variant report

Variant	rs2606065
Chromosome Location	chr2:173495909-173495910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1010752	0.85[ASN][1000 genomes]
rs10181851	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs1075638	0.89[ASN][1000 genomes]
rs10930562	0.81[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs10930565	0.90[ASN][1000 genomes]
rs10930566	0.86[ASN][1000 genomes]
rs10930567	0.86[ASN][1000 genomes]
rs10930568	0.81[ASN][1000 genomes]
rs10930569	0.85[ASN][1000 genomes]
rs1097478	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133602	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11904158	0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs12465512	0.86[ASN][1000 genomes]
rs12476204	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617037	0.81[ASN][1000 genomes]
rs12620518	0.81[ASN][1000 genomes]
rs12693008	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13015260	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13019331	0.90[ASN][1000 genomes]
rs13024563	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13401676	0.93[ASN][1000 genomes]
rs13423020	0.81[ASN][1000 genomes]
rs1531148	0.83[ASN][1000 genomes]
rs1531149	0.83[ASN][1000 genomes]
rs1531150	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16860737	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860741	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868901	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869923	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599261	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599262	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599266	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599267	0.98[AFR][1000 genomes]
rs2599268	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2606062	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2606066	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606070	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606073	0.82[ASN][1000 genomes]
rs28761282	0.80[ASN][1000 genomes]
rs34051646	0.90[ASN][1000 genomes]
rs35892983	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765065	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs3769321	0.81[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs4395226	0.81[ASN][1000 genomes]
rs60127617	0.81[ASN][1000 genomes]
rs62167835	0.88[ASN][1000 genomes]
rs6433376	0.83[ASN][1000 genomes]
rs6710129	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs6718681	0.86[ASN][1000 genomes]
rs6719140	0.86[ASN][1000 genomes]
rs6731354	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733679	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738196	0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs6752386	0.84[ASN][1000 genomes]
rs7584769	0.90[ASN][1000 genomes]
rs836590	1.00[ASN][1000 genomes]
rs836608	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs836614	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs836616	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs836617	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs836620	0.83[CEU][hapmap]
rs836621	0.89[CEU][hapmap]
rs836622	0.88[CEU][hapmap]
rs836623	0.84[CEU][hapmap]
rs836628	0.86[ASN][1000 genomes]
rs836629	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836630	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836631	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836632	0.83[AFR][1000 genomes]
rs836634	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv875415	chr2:173444462-173501069	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875416	chr2:173444462-173504674	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv875417	chr2:173460803-173501069	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875418	chr2:173460803-173504674	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv2762962	chr2:173493078-173527311	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2606065	CYBRD1	cis	parietal	SCAN
rs2606065	LASS6	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173461400-173504200	Weak transcription	NHEK	skin
2	chr2:173462200-173507400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:173472600-173504600	Weak transcription	Adipose Nuclei	Adipose
4	chr2:173474600-173504400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:173478800-173496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:173479600-173496200	Weak transcription	Thymus	Thymus
7	chr2:173479800-173496000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:173480000-173496000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:173480200-173499200	Weak transcription	HepG2	liver
10	chr2:173485800-173497200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:173489200-173496200	Weak transcription	Fetal Thymus	thymus
12	chr2:173489200-173507200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:173489400-173500400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:173489400-173504200	Weak transcription	NHLF	lung
15	chr2:173490200-173500600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:173490400-173497200	Weak transcription	HSMM	muscle
17	chr2:173492800-173497600	Weak transcription	Fetal Brain Female	brain
18	chr2:173494600-173496400	Weak transcription	Fetal Stomach	stomach
19	chr2:173494600-173503800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:173494600-173504200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:173494600-173510200	Weak transcription	Primary T cells from cord blood	blood
22	chr2:173494800-173496400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:173494800-173496400	Weak transcription	Dnd41	blood
24	chr2:173494800-173496800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:173494800-173503800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:173494800-173504400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:173494800-173504400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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