Variant report

Variant	rs9998801
Chromosome Location	chr4:99314167-99314168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10001137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027340	0.87[EUR][1000 genomes]
rs17027393	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	0.80[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027617	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	0.91[AMR][1000 genomes]
rs28494643	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497963	0.82[AMR][1000 genomes]
rs28503871	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28731135	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	1.00[EUR][1000 genomes]
rs28883979	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55993060	0.87[EUR][1000 genomes]
rs56805018	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	0.91[AMR][1000 genomes]
rs60281573	0.87[EUR][1000 genomes]
rs60544326	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60638903	0.87[EUR][1000 genomes]
rs61485715	0.87[EUR][1000 genomes]
rs6831386	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	0.91[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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	0.82[AMR][1000 genomes]
rs7656868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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

No data

Chromatin state (count:82 , 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	chr4:99271600-99314800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:99285000-99337800	Weak transcription	HUVEC	blood vessel
6	chr4:99288400-99342400	Weak transcription	A549	lung
7	chr4:99288800-99319800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:99288800-99329200	Weak transcription	Esophagus	oesophagus
9	chr4:99288800-99332000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:99288800-99333600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:99289000-99314600	Weak transcription	Lung	lung
12	chr4:99289000-99318400	Weak transcription	Ovary	ovary
13	chr4:99289000-99333000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:99289000-99333400	Weak transcription	Pancreas	Pancrea
15	chr4:99289000-99333600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:99289400-99316800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:99289400-99321000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:99290600-99333600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:99290600-99337800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:99290600-99346000	Weak transcription	Fetal Lung	lung
21	chr4:99290800-99315200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:99290800-99316600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:99290800-99317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:99291200-99317000	Weak transcription	Adipose Nuclei	Adipose
25	chr4:99291600-99314600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:99294200-99317000	Weak transcription	Aorta	Aorta
27	chr4:99294800-99333400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:99295000-99315400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:99295400-99316600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:99296000-99333600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:99298600-99318400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr4:99299000-99315200	Weak transcription	HSMMtube	muscle
33	chr4:99299400-99350800	Weak transcription	NHLF	lung
34	chr4:99299600-99338200	Weak transcription	NHDF-Ad	bronchial
35	chr4:99299800-99315400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:99301200-99315200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:99301600-99332000	Weak transcription	Liver	Liver
38	chr4:99301800-99328600	Weak transcription	Fetal Thymus	thymus
39	chr4:99303200-99333400	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:99307000-99333600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:99307000-99366200	Weak transcription	Fetal Brain Male	brain
42	chr4:99307200-99333200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:99307200-99333800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:99308200-99321000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:99308600-99363200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:99308800-99318400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:99308800-99333600	Weak transcription	Psoas Muscle	Psoas
48	chr4:99308800-99333600	Weak transcription	NHEK	skin
49	chr4:99308800-99337800	Weak transcription	Osteobl	bone
50	chr4:99309000-99315200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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