Variant report

Variant	rs2398196
Chromosome Location	chr10:5160045-5160046
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5136589..5138613-chr10:5158907..5161668,2	MCF-7	breast:
2	chr10:5159415..5162131-chr10:5167591..5169595,2	MCF-7	breast:
3	chr10:5157749..5160543-chr10:5164093..5166584,2	MCF-7	breast:
4	chr10:5158412..5160412-chr20:46095387..46097285,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196139	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10752001	0.85[CHB][hapmap]
rs10752005	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10795242	0.85[CHB][hapmap]
rs10795245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10904411	0.84[ASN][1000 genomes]
rs10904417	0.88[ASN][1000 genomes]
rs10904419	0.85[ASN][1000 genomes]
rs10904421	0.85[CHB][hapmap]
rs10904432	0.80[ASN][1000 genomes]
rs11252922	0.85[CHB][hapmap]
rs11253024	0.80[ASN][1000 genomes]
rs11492967	0.80[ASN][1000 genomes]
rs11511661	0.80[ASN][1000 genomes]
rs11511664	0.80[ASN][1000 genomes]
rs11524375	0.80[ASN][1000 genomes]
rs1155931	0.80[ASN][1000 genomes]
rs12355837	0.80[ASN][1000 genomes]
rs12356304	0.80[ASN][1000 genomes]
rs12387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12571915	0.85[ASN][1000 genomes]
rs12775468	1.00[ASN][1000 genomes]
rs12775701	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17134471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17134523	0.85[CHB][hapmap]
rs17307359	0.81[CEU][hapmap]
rs17396032	1.00[AFR][1000 genomes]
rs1761601	0.80[ASN][1000 genomes]
rs1761602	0.80[ASN][1000 genomes]
rs1761603	0.82[ASN][1000 genomes]
rs1761604	0.80[ASN][1000 genomes]
rs1761606	0.80[ASN][1000 genomes]
rs1781927	0.86[ASN][1000 genomes]
rs1781929	0.82[ASN][1000 genomes]
rs1781930	0.82[ASN][1000 genomes]
rs1781933	0.80[ASN][1000 genomes]
rs1781935	0.80[ASN][1000 genomes]
rs1781937	0.80[ASN][1000 genomes]
rs1781938	0.80[ASN][1000 genomes]
rs1781939	0.80[ASN][1000 genomes]
rs1781940	0.80[ASN][1000 genomes]
rs1781941	0.86[ASN][1000 genomes]
rs1892404	1.00[ASN][1000 genomes]
rs1937840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1937841	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1937845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1937847	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1937848	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1937849	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1937882	0.95[ASN][1000 genomes]
rs1937904	0.92[ASN][1000 genomes]
rs1937906	0.92[ASN][1000 genomes]
rs1937916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2154308	0.95[ASN][1000 genomes]
rs2154309	0.92[ASN][1000 genomes]
rs2186175	0.95[ASN][1000 genomes]
rs2211624	0.94[ASN][1000 genomes]
rs2211630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2226260	1.00[ASN][1000 genomes]
rs2298305	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2398103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2398195	1.00[ASN][1000 genomes]
rs2518047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2518049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2801882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2801883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3750573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3812617	0.85[CHB][hapmap]
rs4242785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4330990	0.82[ASN][1000 genomes]
rs4436454	0.92[ASN][1000 genomes]
rs4478887	0.92[ASN][1000 genomes]
rs4622159	1.00[ASN][1000 genomes]
rs4880708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4880710	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4881395	0.83[CHB][hapmap]
rs4881396	0.85[CHB][hapmap]
rs4881397	0.85[CHB][hapmap]
rs4881403	0.97[ASN][1000 genomes]
rs4881404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4881408	0.80[ASN][1000 genomes]
rs4881410	0.80[ASN][1000 genomes]
rs60878270	0.80[ASN][1000 genomes]
rs61854684	0.82[ASN][1000 genomes]
rs61854687	0.82[ASN][1000 genomes]
rs61854697	0.82[ASN][1000 genomes]
rs6601898	0.85[CHB][hapmap]
rs6601899	0.85[CHB][hapmap]
rs6601919	0.80[ASN][1000 genomes]
rs6601920	0.80[ASN][1000 genomes]
rs6601921	0.80[ASN][1000 genomes]
rs6601923	0.80[ASN][1000 genomes]
rs7067921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7070300	0.80[ASN][1000 genomes]
rs7071406	0.80[ASN][1000 genomes]
rs7072750	0.80[ASN][1000 genomes]
rs7074004	0.85[CHB][hapmap]
rs7080497	0.80[ASN][1000 genomes]
rs7087111	0.85[CHB][hapmap]
rs7089964	0.80[ASN][1000 genomes]
rs7090038	0.80[ASN][1000 genomes]
rs7091485	0.92[ASN][1000 genomes]
rs72478267	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72549130	1.00[AFR][1000 genomes]
rs7893682	0.86[ASN][1000 genomes]
rs7898263	0.85[CHB][hapmap]
rs7898341	0.80[ASN][1000 genomes]
rs7901781	0.85[CHB][hapmap]
rs7902978	0.80[ASN][1000 genomes]
rs7907985	0.83[ASN][1000 genomes]
rs7914117	0.97[ASN][1000 genomes]
rs7917079	1.00[ASN][1000 genomes]
rs7918456	0.80[ASN][1000 genomes]
rs7920135	1.00[ASN][1000 genomes]
rs878766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[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	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1047484	chr10:5076258-5261482	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv1042487	chr10:5090313-5196900	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv540463	chr10:5090313-5196900	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv540464	chr10:5108345-5196815	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv540465	chr10:5108345-5261482	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv540466	chr10:5114577-5196815	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv540467	chr10:5114577-5225365	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv540468	chr10:5114577-5261482	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv540469	chr10:5120774-5225365	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv540470	chr10:5120774-5261482	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
27	nsv540471	chr10:5133561-5261482	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv540472	chr10:5133561-5284334	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
29	nsv466714	chr10:5142855-5175450	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
30	nsv549885	chr10:5142855-5175450	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	nsv1047686	chr10:5148453-5185582	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
32	nsv1048081	chr10:5149144-5321395	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5148600-5160200	Weak transcription	Stomach Mucosa	stomach
2	chr10:5151000-5178000	Weak transcription	Adipose Nuclei	Adipose
3	chr10:5156400-5160200	Strong transcription	Liver	Liver
4	chr10:5157600-5160400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr10:5157600-5161000	Enhancers	Primary hematopoietic stem cells	blood
6	chr10:5159000-5160800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:5159600-5160800	Enhancers	HepG2	liver
8	chr10:5159800-5160600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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