Variant report

Variant	rs2255039
Chromosome Location	chr2:128394758-128394759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128394527..128396772-chr2:128458451..128460497,2	MCF-7	breast:
2	chr2:128386978..128389867-chr2:128392766..128396164,5	MCF-7	breast:
3	chr2:128280589..128286553-chr2:128394118..128400117,7	K562	blood:
4	chr2:128282410..128284022-chr2:128394708..128396398,2	MCF-7	breast:
5	chr2:128393595..128398988-chr2:128401355..128406842,9	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIMS2-1	chr2:128394380-128394796	NONHSAT074176

No data

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction
ENSG00000072163	Chromatin interaction
ENSG00000173349	Chromatin interaction
ENSG00000144230	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10183797	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10186397	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10208043	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2244871	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244880	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2255177	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011937	chr2:128295320-128405921	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1008294	chr2:128295320-128420654	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1007207	chr2:128295320-128429775	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1003004	chr2:128295320-128474326	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv1008457	chr2:128299079-128405921	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1009514	chr2:128299079-128420654	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1006421	chr2:128299079-128473079	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1004877	chr2:128299079-128479640	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv875015	chr2:128305196-128495645	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1001624	chr2:128306660-128420654	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv875016	chr2:128330458-128401091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv875017	chr2:128330458-128445585	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv875018	chr2:128330458-128465547	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv518085	chr2:128334413-128404860	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv583037	chr2:128334470-128401091	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv875019	chr2:128340855-128408170	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv875020	chr2:128340855-128445585	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv875021	chr2:128340855-128465547	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
19	nsv470482	chr2:128350808-128465547	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
20	esv3368061	chr2:128375044-128672849	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	60 gene(s)	inside rSNPs	diseases
21	nsv875022	chr2:128378563-128405721	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv875023	chr2:128378563-128407499	Bivalent Enhancer Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv875024	chr2:128378563-128408170	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
24	nsv875025	chr2:128378563-128409419	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv875026	chr2:128378563-128445585	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
26	nsv428726	chr2:128387756-128539894	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
27	nsv517532	chr2:128387937-128404860	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv875027	chr2:128387937-128408170	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
29	nsv875028	chr2:128387937-128445585	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2255039	MYO7B	cis	Whole Blood	GTEx
rs2255039	LIMS2	cis	Whole Blood	GTEx
rs2255039	GPR17	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128359200-128395200	Strong transcription	Duodenum Mucosa	Duodenum
2	chr2:128386200-128396000	Enhancers	Fetal Thymus	thymus
3	chr2:128386400-128395600	Enhancers	Primary B cells from cord blood	blood
4	chr2:128387400-128396400	Enhancers	Placenta	Placenta
5	chr2:128388000-128394800	Enhancers	Adipose Nuclei	Adipose
6	chr2:128388000-128395000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr2:128388600-128395000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:128388800-128395000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:128389000-128394800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:128389800-128395200	Enhancers	Primary T cells from cord blood	blood
11	chr2:128390000-128397200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr2:128390400-128395400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:128390800-128398400	Genic enhancers	Fetal Intestine Small	intestine
14	chr2:128391200-128395600	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:128391400-128395000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:128391400-128396200	Genic enhancers	Spleen	Spleen
17	chr2:128391600-128395000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:128391600-128395000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:128391600-128397200	Genic enhancers	Fetal Intestine Large	intestine
20	chr2:128391800-128394800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:128392000-128396600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:128392000-128397400	Weak transcription	Brain Angular Gyrus	brain
23	chr2:128392000-128397400	Weak transcription	GM12878-XiMat	blood
24	chr2:128392000-128403000	Weak transcription	Brain Germinal Matrix	brain
25	chr2:128392200-128394800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:128392200-128394800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:128392200-128394800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:128392200-128394800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:128392200-128395000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:128392200-128395000	Weak transcription	Fetal Lung	lung
31	chr2:128392200-128395200	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:128392200-128395600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:128392200-128395600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:128392200-128397400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:128392200-128400400	Weak transcription	Brain Substantia Nigra	brain
36	chr2:128392400-128395000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:128392400-128395400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:128392400-128402000	Genic enhancers	Right Ventricle	heart
39	chr2:128392600-128394800	Weak transcription	Pancreas	Pancrea
40	chr2:128392600-128400800	Enhancers	Primary B cells from peripheral blood	blood
41	chr2:128392800-128395200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:128392800-128399000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr2:128393000-128395000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr2:128393000-128395200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr2:128393000-128395400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:128393000-128396000	Enhancers	Right Atrium	heart
47	chr2:128393200-128400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:128393400-128394800	Weak transcription	Stomach Mucosa	stomach
49	chr2:128393400-128395000	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr2:128393400-128395400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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