Variant report

Variant	rs4952644
Chromosome Location	chr2:40948769-40948770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11124756	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11491284	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11689010	0.87[ASN][1000 genomes]
rs11887013	0.81[EUR][1000 genomes]
rs11898380	0.81[ASN][1000 genomes]
rs11899009	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469563	0.88[ASN][1000 genomes]
rs12474948	0.85[EUR][1000 genomes]
rs12477643	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12712704	0.82[ASN][1000 genomes]
rs12712709	0.87[ASN][1000 genomes]
rs1541575	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026319	0.85[EUR][1000 genomes]
rs17026434	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17026446	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17026537	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026541	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026544	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026584	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026612	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17026616	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17026644	0.92[ASN][1000 genomes]
rs1861307	0.87[ASN][1000 genomes]
rs1990617	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2005413	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052260	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2160262	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2216043	0.87[ASN][1000 genomes]
rs2888699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911438	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3915716	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs42787	0.85[EUR][1000 genomes]
rs4597578	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4610094	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952643	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022306	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56407568	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57225071	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57569001	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57770208	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57955071	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57988012	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59892061	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60373384	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61275311	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544345	0.81[ASN][1000 genomes]
rs72945712	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7369946	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7369960	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7423585	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7581499	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7608684	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873931	chr2:40869165-40966719	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv456441	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv581514	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv456452	chr2:40890416-40989061	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv581515	chr2:40890416-40989061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3584751	chr2:40916853-40952073	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
16	esv2754698	chr2:40922098-40949606	Flanking Active TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
17	esv34871	chr2:40922098-40951667	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
18	esv2755242	chr2:40922098-40951667	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
19	esv3584750	chr2:40926091-40949606	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
20	esv3457577	chr2:40926899-40949434	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
21	esv3457576	chr2:40926923-40949434	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
22	esv3457575	chr2:40926941-40949439	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
23	nsv829008	chr2:40927002-40949224	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv829019	chr2:40927002-40949304	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
25	esv3457578	chr2:40927064-40949267	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
26	nsv1004050	chr2:40927363-40949606	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
27	nsv441754	chr2:40927375-40949602	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
28	esv3584749	chr2:40927375-40949606	Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
29	nsv514064	chr2:40929032-40949156	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
30	nsv961752	chr2:40929037-40950223	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
31	esv2756918	chr2:40930721-40966719	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
32	esv2759045	chr2:40930721-40966719	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40944600-40948800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40944600-40949000	Weak transcription	Osteobl	bone
3	chr2:40944600-40949600	Weak transcription	Esophagus	oesophagus
4	chr2:40946600-40948800	Weak transcription	HSMM	muscle
5	chr2:40947000-40951200	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:40947000-40952400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:40948400-40949400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:40948400-40949400	Enhancers	NHEK	skin
9	chr2:40948600-40949200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:40948600-40949200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:40948600-40949400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:40948600-40949400	Enhancers	HMEC	breast
13	chr2:40948600-40949400	Enhancers	HSMMtube	muscle
14	chr2:40948600-40949600	Enhancers	NHDF-Ad	bronchial
15	chr2:40948600-40949800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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