Variant report

Variant	rs10865278
Chromosome Location	chr2:54302039-54302040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1058320	0.88[CHB][hapmap]
rs1075265	0.88[CHB][hapmap]
rs10865277	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865279	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125520	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11683654	0.82[YRI][hapmap]
rs11695734	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11887549	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11896781	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1363062	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs1363063	0.86[JPT][hapmap]
rs1421617	0.86[JPT][hapmap]
rs1559037	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17045474	0.85[YRI][hapmap]
rs1833497	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1862121	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1862122	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2018747	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2287642	0.82[CHB][hapmap]
rs2357954	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34769118	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41385746	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671178	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671190	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4671872	0.88[CHB][hapmap]
rs56001939	0.85[AMR][1000 genomes]
rs62137965	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62137973	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6545384	0.80[ASN][1000 genomes]
rs6545388	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs6741891	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7558126	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7566894	0.82[CHB][hapmap]
rs7590846	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7600141	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604357	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs888635	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs918357	0.82[CHB][hapmap];0.89[CHD][hapmap];0.80[MEX][hapmap]
rs929734	0.82[CHB][hapmap]
rs959285	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10865278	ACYP2	cis	multi-tissue	Pritchard
rs10865278	MTIF2	cis	cerebellum	SCAN
rs10865278	PSME4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54278800-54302400	Weak transcription	Left Ventricle	heart
2	chr2:54280800-54310000	Weak transcription	Ovary	ovary
3	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
4	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
6	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
9	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
10	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:54291800-54304800	Weak transcription	Fetal Kidney	kidney
12	chr2:54292000-54308400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:54293000-54306000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:54293200-54306200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:54293200-54306200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:54293400-54308400	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:54293600-54310600	Weak transcription	HSMM	muscle
18	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine
19	chr2:54295200-54312200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:54295400-54309800	Weak transcription	Fetal Brain Male	brain
21	chr2:54300400-54302200	Enhancers	Hela-S3	cervix
22	chr2:54300600-54302200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:54300600-54302200	Enhancers	NHEK	skin
24	chr2:54300800-54302200	Enhancers	HUVEC	blood vessel
25	chr2:54301000-54302200	Enhancers	HMEC	breast
26	chr2:54301000-54303400	Enhancers	K562	blood
27	chr2:54301400-54302600	Enhancers	NH-A	brain
28	chr2:54301400-54303800	Weak transcription	Pancreas	Pancrea
29	chr2:54301400-54304200	Weak transcription	GM12878-XiMat	blood
30	chr2:54301600-54308200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:54301800-54302200	Enhancers	Spleen	Spleen
32	chr2:54302000-54302200	Enhancers	Fetal Heart	heart
33	chr2:54302000-54302200	Enhancers	A549	lung
34	chr2:54302000-54302600	Enhancers	Osteobl	bone

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