Variant report

Variant	rs16827148
Chromosome Location	chr2:231222340-231222341
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12615773	0.81[ASN][1000 genomes]
rs16827136	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56291657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62192168	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6742592	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs6742630	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7579078	0.86[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv3417154	chr2:231159789-231258938	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004183	chr2:231174420-231258603	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1013738	chr2:231176856-231258603	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv584667	chr2:231177822-231258450	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv460119	chr2:231178876-231258450	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv584668	chr2:231178876-231258450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1001929	chr2:231179884-231258603	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv584669	chr2:231183321-231258150	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv584670	chr2:231183786-231241276	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv3374323	chr2:231186424-231244177	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv819175	chr2:231214969-231222711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16827148	ARMC9	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231192800-231223800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:231193600-231224000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:231194000-231222600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:231200600-231224000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:231201800-231223200	Weak transcription	HSMM	muscle
6	chr2:231211000-231222400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:231211200-231223200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:231212400-231222400	Weak transcription	Ovary	ovary
9	chr2:231212400-231224000	Weak transcription	Thymus	Thymus
10	chr2:231212400-231225200	Weak transcription	Lung	lung
11	chr2:231212600-231222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:231212600-231222600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:231212600-231222600	Weak transcription	Placenta	Placenta
14	chr2:231212600-231223200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:231212600-231224600	Weak transcription	Esophagus	oesophagus
16	chr2:231212600-231225200	Weak transcription	Fetal Stomach	stomach
17	chr2:231212600-231226000	Weak transcription	Pancreas	Pancrea
18	chr2:231212800-231222600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:231212800-231222600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:231212800-231223000	Weak transcription	Fetal Thymus	thymus
21	chr2:231212800-231223200	Weak transcription	Left Ventricle	heart
22	chr2:231212800-231223800	Weak transcription	Aorta	Aorta
23	chr2:231212800-231224800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:231212800-231225600	Weak transcription	Spleen	Spleen
25	chr2:231212800-231235600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:231212800-231236600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:231212800-231253600	Weak transcription	Gastric	stomach
28	chr2:231212800-231253600	Weak transcription	HMEC	breast
29	chr2:231212800-231259200	Weak transcription	Small Intestine	intestine
30	chr2:231212800-231262400	Weak transcription	K562	blood
31	chr2:231213000-231222400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:231213000-231222400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:231213000-231222400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:231213000-231222600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr2:231213000-231222800	Weak transcription	NH-A	brain
36	chr2:231213000-231223600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:231213000-231237600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:231213200-231222400	Weak transcription	Dnd41	blood
39	chr2:231214200-231223200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:231214400-231222400	Weak transcription	GM12878-XiMat	blood
41	chr2:231214600-231222400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:231215600-231223000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:231215800-231223000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:231216000-231222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:231216200-231226000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:231216600-231222400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:231216800-231222600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:231217200-231222400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:231219400-231222600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:231219600-231222400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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