Variant report

Variant	rs843672
Chromosome Location	chr2:54417645-54417646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1682102	0.83[CHB][hapmap]
rs1682108	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1682111	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1727504	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1727527	0.87[ASN][1000 genomes]
rs698752	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap]
rs7574477	0.80[YRI][hapmap]
rs843648	0.81[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs843666	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs843671	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs843720	0.83[CHB][hapmap]
rs843721	0.83[CHB][hapmap]
rs843722	0.83[CHB][hapmap]
rs843730	0.83[CHB][hapmap]
rs843731	0.83[CHB][hapmap]
rs843740	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs843754	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs843764	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs843765	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs863622	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1003889	chr2:54347750-54424601	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1011433	chr2:54351145-54424601	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1012230	chr2:54351988-54422959	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv874149	chr2:54358517-54432222	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv961316	chr2:54409849-54427030	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs843672	RTN4	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54380600-54429200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:54380600-54434400	Weak transcription	Ovary	ovary
3	chr2:54387800-54457400	Weak transcription	Aorta	Aorta
4	chr2:54388400-54424600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:54388400-54435000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:54389800-54420000	Weak transcription	Fetal Stomach	stomach
7	chr2:54404200-54433600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:54406400-54419600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:54410000-54420000	Weak transcription	Right Atrium	heart
10	chr2:54411200-54423600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:54412200-54422200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:54412600-54422600	Weak transcription	Fetal Lung	lung
13	chr2:54412600-54435000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:54412800-54417800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:54413000-54420000	Weak transcription	Spleen	Spleen
16	chr2:54414200-54434600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:54415000-54418200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:54415200-54432400	Weak transcription	Primary B cells from cord blood	blood
19	chr2:54415200-54434200	Weak transcription	Primary T cells from cord blood	blood
20	chr2:54415200-54434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:54415200-54434600	Weak transcription	HSMMtube	muscle
22	chr2:54415400-54434400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:54416200-54419800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:54416200-54420000	Weak transcription	Fetal Intestine Small	intestine
25	chr2:54416200-54420400	Weak transcription	Liver	Liver
26	chr2:54416200-54421200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:54416200-54451400	Weak transcription	Left Ventricle	heart
28	chr2:54416400-54427600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:54417000-54425800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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