Variant report

Variant	rs2248661
Chromosome Location	chr2:128376401-128376402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10164978	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10174611	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183797	0.95[ASN][1000 genomes]
rs10186397	0.94[ASN][1000 genomes]
rs10208043	0.95[ASN][1000 genomes]
rs1852708	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2244880	0.95[ASN][1000 genomes]
rs2245711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248754	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255177	0.82[ASN][1000 genomes]
rs6708915	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2248661	LIMS2	cis	Whole Blood	GTEx
rs2248661	GPR17	cis	Artery Tibial	GTEx
rs2248661	MYO7B	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128359200-128395200	Strong transcription	Duodenum Mucosa	Duodenum
2	chr2:128370400-128377000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:128371000-128391600	Strong transcription	Fetal Intestine Large	intestine
4	chr2:128371400-128390800	Strong transcription	Fetal Intestine Small	intestine
5	chr2:128371800-128378400	Enhancers	Fetal Thymus	thymus
6	chr2:128372600-128378600	Weak transcription	Colonic Mucosa	Colon
7	chr2:128372800-128377000	Weak transcription	Spleen	Spleen
8	chr2:128373000-128380800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:128373200-128379400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:128374400-128377000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:128374600-128377400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:128374800-128377600	Genic enhancers	Dnd41	blood
13	chr2:128375000-128377200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:128375000-128377800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:128375400-128377000	Weak transcription	Primary B cells from cord blood	blood
16	chr2:128375600-128377000	Weak transcription	Small Intestine	intestine
17	chr2:128375600-128378000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:128375800-128376600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:128375800-128376800	Enhancers	Placenta	Placenta
20	chr2:128376000-128376600	Enhancers	Fetal Muscle Leg	muscle
21	chr2:128376000-128379200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:128376200-128376600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:128376200-128376600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:128376200-128376600	Enhancers	HSMM	muscle
25	chr2:128376200-128376600	Enhancers	HSMMtube	muscle
26	chr2:128376200-128376800	Enhancers	Primary hematopoietic stem cells	blood
27	chr2:128376200-128376800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:128376400-128376600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:128376400-128376600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:128376400-128376600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr2:128376400-128376800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:128376400-128377600	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:128376400-128379000	Enhancers	Thymus	Thymus

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