Variant report

Variant	rs10025311
Chromosome Location	chr4:99297897-99297898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr4:99297500-99297915	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RAP1GDS1	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10001137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027340	0.87[EUR][1000 genomes]
rs17027388	0.80[AMR][1000 genomes]
rs17027393	0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	1.00[AMR][1000 genomes]
rs28494643	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497963	0.91[AMR][1000 genomes]
rs28503871	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705201	0.80[AMR][1000 genomes]
rs28731135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28883979	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55993060	0.87[EUR][1000 genomes]
rs56805018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	1.00[AMR][1000 genomes]
rs60281573	0.87[EUR][1000 genomes]
rs60544326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60638903	0.87[EUR][1000 genomes]
rs61485715	0.87[EUR][1000 genomes]
rs6831386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832142	0.87[EUR][1000 genomes]
rs73832145	0.87[EUR][1000 genomes]
rs73832149	0.87[EUR][1000 genomes]
rs73832156	0.87[EUR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	0.94[YRI][hapmap];0.91[AMR][1000 genomes]
rs7656868	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv999097	chr4:99271563-99304326	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1012360	chr4:99271563-99308481	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1010207	chr4:99291295-99312807	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99215000-99317000	Weak transcription	Left Ventricle	heart
2	chr4:99262800-99333400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:99264200-99338200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:99265400-99298400	Weak transcription	NHDF-Ad	bronchial
5	chr4:99271600-99314800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:99280000-99298600	Weak transcription	NHLF	lung
7	chr4:99285000-99337800	Weak transcription	HUVEC	blood vessel
8	chr4:99285200-99306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:99286400-99310200	Weak transcription	Small Intestine	intestine
10	chr4:99288400-99342400	Weak transcription	A549	lung
11	chr4:99288600-99298600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:99288600-99313000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:99288800-99319800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:99288800-99329200	Weak transcription	Esophagus	oesophagus
15	chr4:99288800-99332000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:99288800-99333600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:99289000-99298000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:99289000-99298400	Strong transcription	Dnd41	blood
19	chr4:99289000-99301000	Weak transcription	Liver	Liver
20	chr4:99289000-99313600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:99289000-99314600	Weak transcription	Lung	lung
22	chr4:99289000-99318400	Weak transcription	Ovary	ovary
23	chr4:99289000-99333000	Weak transcription	Fetal Intestine Large	intestine
24	chr4:99289000-99333400	Weak transcription	Pancreas	Pancrea
25	chr4:99289000-99333600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:99289400-99316800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:99289400-99321000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:99290400-99308200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:99290400-99308600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr4:99290400-99308600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:99290600-99312800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:99290600-99333600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:99290600-99337800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:99290600-99346000	Weak transcription	Fetal Lung	lung
35	chr4:99290800-99302400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:99290800-99308400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:99290800-99313000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:99290800-99315200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:99290800-99316600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:99290800-99317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:99291200-99308600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:99291200-99317000	Weak transcription	Adipose Nuclei	Adipose
43	chr4:99291600-99314600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:99292200-99307600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:99292800-99308600	Weak transcription	Primary T cells from cord blood	blood
46	chr4:99292800-99313600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:99293000-99301200	Weak transcription	Fetal Thymus	thymus
48	chr4:99293400-99308200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:99294200-99317000	Weak transcription	Aorta	Aorta
50	chr4:99294800-99333400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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