Variant report

Variant	rs7583955
Chromosome Location	chr2:231033288-231033289
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-2	chr2:231032009-231033953	NONHSAT077261

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10210254	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1060759	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137604	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137605	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12328528	0.89[ASN][1000 genomes]
rs13026113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13026121	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13026878	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2114586	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731723	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3731725	0.89[ASN][1000 genomes]
rs3943889	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4283410	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4381771	0.89[ASN][1000 genomes]
rs4624369	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4973278	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4973279	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4973280	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4973281	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4973282	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4973283	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6436917	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs722555	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9288658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957683	0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7583955	SP110	cis	brain	BrainEAC

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231024800-231036400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:231025000-231033800	Weak transcription	Small Intestine	intestine
3	chr2:231025000-231034200	Weak transcription	Brain Substantia Nigra	brain
4	chr2:231025000-231034400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:231025000-231034400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:231025000-231034400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:231025000-231034400	Weak transcription	Pancreas	Pancrea
8	chr2:231025000-231034600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:231025000-231034800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:231025000-231035000	Weak transcription	Placenta	Placenta
11	chr2:231025000-231035400	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:231025000-231036200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:231025000-231036200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:231025000-231036600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:231025000-231036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:231025000-231036600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:231025000-231036600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:231025000-231040000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:231025400-231035000	Weak transcription	Right Ventricle	heart
20	chr2:231026200-231036200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:231026400-231036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:231026400-231041600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:231026400-231041800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:231026600-231035000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:231026600-231037000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:231026600-231040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:231026600-231041400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:231028200-231036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:231028400-231034400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:231028400-231034400	Strong transcription	Primary T cells from cord blood	blood
31	chr2:231028400-231035000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:231028400-231067000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:231028600-231039600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:231028600-231051200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:231028800-231034000	Weak transcription	Colonic Mucosa	Colon
36	chr2:231028800-231035400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:231028800-231051600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:231029200-231033800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:231029800-231035400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:231030600-231033600	Weak transcription	Fetal Stomach	stomach
41	chr2:231030600-231036200	Weak transcription	Esophagus	oesophagus
42	chr2:231030800-231035000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:231030800-231051000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:231030800-231051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:231031000-231036400	Weak transcription	Fetal Lung	lung
46	chr2:231031000-231040600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:231031200-231036200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:231031200-231049800	Weak transcription	HSMMtube	muscle
49	chr2:231031400-231034600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:231031400-231035000	Strong transcription	Primary monocytes fromperipheralblood	blood

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