Variant report

Variant	rs11884857
Chromosome Location	chr2:54260322-54260323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-4	chr2:54259644-54261288	NONHSAT070722

Extended variants
information (count: 86 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1001296	1.00[CHB][hapmap]
rs10181332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs10188834	0.83[AMR][1000 genomes]
rs10190353	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193846	0.89[EUR][1000 genomes]
rs10199041	1.00[CHB][hapmap]
rs10199995	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10207892	1.00[CHB][hapmap]
rs10208649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496027	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs1049894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs11125517	0.83[AMR][1000 genomes]
rs11125521	1.00[CHB][hapmap]
rs11884327	1.00[CHB][hapmap]
rs11886366	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11887593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11890472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11891079	1.00[CHB][hapmap]
rs11896279	1.00[CHB][hapmap]
rs11903396	0.90[AFR][1000 genomes]
rs11904365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13382454	0.88[AFR][1000 genomes]
rs13390377	1.00[CHB][hapmap]
rs13395751	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13401491	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs13414565	1.00[CHB][hapmap]
rs13417051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs13425337	1.00[CHB][hapmap]
rs13432387	0.88[AMR][1000 genomes]
rs17039541	0.95[YRI][hapmap]
rs17045513	1.00[CHB][hapmap]
rs17045575	1.00[CHB][hapmap]
rs17045645	1.00[CHB][hapmap]
rs17189680	1.00[CHB][hapmap]
rs1872328	1.00[CHB][hapmap]
rs2090182	1.00[CHB][hapmap]
rs2112120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161083	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571698	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28699646	0.88[AMR][1000 genomes]
rs3930909	0.86[AFR][1000 genomes]
rs41536750	0.88[AMR][1000 genomes]
rs4553857	1.00[CHB][hapmap]
rs58920915	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60769690	0.83[AMR][1000 genomes]
rs60776154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545382	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711310	0.85[AFR][1000 genomes]
rs6715161	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6719990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6723722	0.94[AMR][1000 genomes]
rs6730494	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6731217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6745729	0.88[AMR][1000 genomes]
rs6748686	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6756424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72904915	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906704	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906711	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906714	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906778	0.89[EUR][1000 genomes]
rs72906786	0.89[EUR][1000 genomes]
rs72906787	0.89[EUR][1000 genomes]
rs7556936	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7567556	1.00[CHB][hapmap]
rs7567614	1.00[CHB][hapmap]
rs7583508	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588134	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7588319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594400	1.00[CHB][hapmap]
rs7604464	1.00[CHB][hapmap]
rs7608085	0.88[AMR][1000 genomes]
rs9678301	0.88[AMR][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	nsv963232	chr2:54249008-54261054	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	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
9	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

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54243800-54268000	Weak transcription	Osteobl	bone
2	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
4	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
7	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:54251600-54263800	Weak transcription	Primary T cells from cord blood	blood
9	chr2:54254600-54267400	Weak transcription	Brain Substantia Nigra	brain
10	chr2:54254600-54269800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:54254800-54269600	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:54258000-54272200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:54258200-54264400	Weak transcription	Fetal Brain Female	brain
14	chr2:54258200-54266200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:54258200-54266400	Weak transcription	Psoas Muscle	Psoas
16	chr2:54258200-54267000	Weak transcription	Ovary	ovary
17	chr2:54258200-54269600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:54258200-54269800	Weak transcription	Fetal Heart	heart
19	chr2:54258200-54269800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:54258200-54270000	Weak transcription	HepG2	liver
21	chr2:54259000-54267200	Weak transcription	Adipose Nuclei	Adipose
22	chr2:54260000-54260400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr2:54260000-54269800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:54260000-54272200	Weak transcription	Primary B cells from peripheral blood	blood

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