Variant report

Variant	rs10904417
Chromosome Location	chr10:5142423-5142424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5139751..5141653-chr10:5142229..5144051,2	K562	blood:
2	chr10:5140998..5143202-chr10:5149820..5152620,2	K562	blood:
3	chr10:5135730..5138479-chr10:5140412..5142462,2	K562	blood:
4	chr10:5140565..5143325-chr10:5148088..5150883,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239142	Chromatin interaction
ENSG00000196139	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10752005	0.88[ASN][1000 genomes]
rs10795245	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10904411	0.84[ASN][1000 genomes]
rs10904419	0.88[ASN][1000 genomes]
rs10904432	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11253024	0.82[AMR][1000 genomes]
rs11492967	0.83[AMR][1000 genomes]
rs11511661	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11511664	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1155931	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12355837	0.83[AMR][1000 genomes]
rs12355966	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12356304	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12387	0.94[ASN][1000 genomes]
rs12529	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12571915	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12775468	0.88[ASN][1000 genomes]
rs1761601	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1761602	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1761606	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1781927	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1781935	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1781937	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1781940	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1781941	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1892404	0.88[ASN][1000 genomes]
rs1937840	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1937841	0.94[ASN][1000 genomes]
rs1937845	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1937847	0.94[ASN][1000 genomes]
rs1937848	0.94[ASN][1000 genomes]
rs1937849	0.94[ASN][1000 genomes]
rs1937882	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1937904	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1937906	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1937916	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2154308	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2154309	0.95[ASN][1000 genomes]
rs2186175	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2211624	0.94[ASN][1000 genomes]
rs2226260	0.88[ASN][1000 genomes]
rs2298305	0.95[ASN][1000 genomes]
rs2398103	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2398195	0.88[ASN][1000 genomes]
rs2398196	0.88[ASN][1000 genomes]
rs2518047	0.95[ASN][1000 genomes]
rs2518049	0.95[ASN][1000 genomes]
rs2801882	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2801883	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4242785	0.97[ASN][1000 genomes]
rs4436454	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4478887	0.95[ASN][1000 genomes]
rs4622159	0.88[ASN][1000 genomes]
rs4880708	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4880710	0.85[ASN][1000 genomes]
rs4881403	0.85[ASN][1000 genomes]
rs4881404	0.85[ASN][1000 genomes]
rs4881408	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4881410	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6601919	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6601920	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6601921	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7070300	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7071406	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7072048	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7080497	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7089964	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7091485	0.95[ASN][1000 genomes]
rs7893682	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7898341	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7907985	0.83[ASN][1000 genomes]
rs7914117	0.85[ASN][1000 genomes]
rs7917079	0.88[ASN][1000 genomes]
rs7918456	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7920135	0.88[ASN][1000 genomes]
rs878766	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5136600-5147400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:5137200-5145200	Weak transcription	Esophagus	oesophagus
3	chr10:5137200-5145800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:5137200-5149800	Weak transcription	Small Intestine	intestine
5	chr10:5137400-5149400	Weak transcription	HSMM	muscle
6	chr10:5137400-5149600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:5137400-5149600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:5137400-5149800	Weak transcription	Pancreas	Pancrea
9	chr10:5137400-5151600	Weak transcription	Brain Angular Gyrus	brain
10	chr10:5137400-5151800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:5137400-5152000	Weak transcription	Right Ventricle	heart
12	chr10:5137600-5147800	Weak transcription	HMEC	breast
13	chr10:5137800-5150800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:5138000-5147200	Transcr. at gene 5' and 3'	A549	lung
15	chr10:5138200-5146800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr10:5138200-5148400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr10:5138200-5151000	Weak transcription	Osteobl	bone
18	chr10:5138200-5151800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr10:5138600-5145000	Weak transcription	Gastric	stomach
20	chr10:5138600-5145200	Weak transcription	Ovary	ovary
21	chr10:5138600-5149200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:5138600-5149800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:5138600-5150200	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:5138600-5151800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr10:5138800-5147800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr10:5138800-5151800	Weak transcription	Brain Anterior Caudate	brain
27	chr10:5138800-5151800	Weak transcription	Colonic Mucosa	Colon
28	chr10:5138800-5152000	Weak transcription	Psoas Muscle	Psoas
29	chr10:5139000-5151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:5139600-5142600	Strong transcription	Left Ventricle	heart
31	chr10:5139600-5142800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr10:5139600-5146000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr10:5139600-5147000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:5140000-5144400	Strong transcription	NHDF-Ad	bronchial
35	chr10:5140000-5148200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:5140200-5143200	Strong transcription	Hela-S3	cervix
37	chr10:5140200-5148200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:5140200-5150400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr10:5140800-5148600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:5140800-5149800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:5141000-5145600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:5141200-5142600	Strong transcription	Lung	lung
43	chr10:5141200-5145600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr10:5141600-5145200	Weak transcription	Stomach Mucosa	stomach
45	chr10:5141600-5145600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:5141800-5144800	Weak transcription	Thymus	Thymus
47	chr10:5141800-5147400	Strong transcription	Liver	Liver
48	chr10:5141800-5147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr10:5142000-5144800	Weak transcription	Aorta	Aorta
50	chr10:5142000-5145200	Weak transcription	HSMMtube	muscle

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