Variant report

Variant	rs4269803
Chromosome Location	chr1:98383165-98383166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:98382961..98385370-chr1:98386122..98388723,2	K562	blood:
2	chr1:98375273..98377235-chr1:98382910..98385584,2	K562	blood:

Variant related genes	Relation type
ENSG00000188641	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10735795	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10747494	0.90[ASW][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10875119	0.89[ASW][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11165918	1.00[AMR][1000 genomes]
rs11165926	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1333721	0.83[YRI][hapmap]
rs1333722	1.00[EUR][1000 genomes]
rs17100628	0.90[ASW][hapmap];0.91[YRI][hapmap]
rs17117167	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs17117173	0.91[YRI][hapmap]
rs17117175	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs17117176	0.90[YRI][hapmap]
rs17117179	0.91[YRI][hapmap]
rs17117181	0.90[ASW][hapmap];0.91[YRI][hapmap]
rs17117194	0.90[ASW][hapmap];0.91[YRI][hapmap]
rs17117198	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs17117203	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs17117207	0.83[YRI][hapmap]
rs17117211	0.91[YRI][hapmap]
rs17117214	0.81[YRI][hapmap]
rs17117218	0.83[YRI][hapmap]
rs17117228	0.83[YRI][hapmap]
rs17117234	0.83[YRI][hapmap]
rs17117251	0.90[ASW][hapmap];0.91[YRI][hapmap]
rs17117438	1.00[EUR][1000 genomes]
rs17117480	1.00[EUR][1000 genomes]
rs17117486	1.00[EUR][1000 genomes]
rs17117488	1.00[EUR][1000 genomes]
rs17117490	1.00[EUR][1000 genomes]
rs17117528	1.00[EUR][1000 genomes]
rs1855376	0.83[YRI][hapmap]
rs4304628	1.00[ASW][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4348763	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs4351683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4367807	0.89[ASW][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs4592283	1.00[EUR][1000 genomes]
rs55989986	1.00[EUR][1000 genomes]
rs56996093	1.00[AMR][1000 genomes]
rs57429463	1.00[EUR][1000 genomes]
rs57957567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58211735	1.00[EUR][1000 genomes]
rs58260707	1.00[EUR][1000 genomes]
rs58615096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59429666	1.00[EUR][1000 genomes]
rs60366086	1.00[EUR][1000 genomes]
rs6604092	0.89[ASW][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6604119	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74105297	1.00[EUR][1000 genomes]
rs74105460	1.00[EUR][1000 genomes]
rs74106015	1.00[EUR][1000 genomes]
rs74106050	1.00[EUR][1000 genomes]
rs74106053	1.00[EUR][1000 genomes]
rs74106056	1.00[EUR][1000 genomes]
rs74106140	1.00[EUR][1000 genomes]
rs74107712	1.00[EUR][1000 genomes]
rs74108221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74108405	1.00[EUR][1000 genomes]
rs74108407	1.00[EUR][1000 genomes]
rs7511709	1.00[ASW][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545029	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs7546038	0.82[ASW][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7553943	0.89[ASW][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9324376	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9324377	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs9661407	0.89[ASW][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9727974	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9729900	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98368000-98384000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:98369800-98384000	Weak transcription	Right Atrium	heart
3	chr1:98371200-98383200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:98373200-98383800	Weak transcription	Hela-S3	cervix
5	chr1:98373200-98384400	Weak transcription	NH-A	brain
6	chr1:98373600-98383400	Weak transcription	HUVEC	blood vessel
7	chr1:98373600-98384400	Weak transcription	A549	lung
8	chr1:98377600-98385000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:98377800-98383400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:98377800-98383400	Weak transcription	Thymus	Thymus
11	chr1:98377800-98383800	Weak transcription	Fetal Thymus	thymus
12	chr1:98377800-98385400	Weak transcription	Small Intestine	intestine
13	chr1:98378000-98383200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:98378000-98383800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:98378600-98383200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:98380400-98383200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:98380600-98383400	Weak transcription	Fetal Lung	lung
18	chr1:98381400-98384600	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:98381400-98385000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:98381600-98383200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:98381800-98383400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:98382000-98384800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:98382000-98385200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr1:98382200-98383200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:98382200-98383400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:98382200-98383800	Enhancers	Osteobl	bone
27	chr1:98382200-98384000	Enhancers	Primary T cells from cord blood	blood
28	chr1:98382200-98384000	Enhancers	Liver	Liver
29	chr1:98382200-98384600	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:98382200-98384600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:98382200-98384600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:98382200-98384600	Enhancers	Brain Hippocampus Middle	brain
33	chr1:98382200-98384800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:98382200-98385800	Active TSS	Fetal Brain Female	brain
35	chr1:98382400-98383400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:98382400-98383800	Active TSS	GM12878-XiMat	blood
37	chr1:98382400-98384600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:98382400-98384800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr1:98382600-98383200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:98382600-98383200	Weak transcription	Brain Angular Gyrus	brain
41	chr1:98382600-98383800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:98382600-98384800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:98382800-98383400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:98382800-98384000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:98382800-98384600	Enhancers	Adipose Nuclei	Adipose
46	chr1:98382800-98384800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:98382800-98384800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr1:98382800-98385200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:98383000-98383200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:98383000-98383200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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