Variant report

Variant	rs60828800
Chromosome Location	chr2:98582030-98582031
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	chr2:98580682..98582944-chr2:98610154..98612049,2	K562	blood:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11892146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	1.00[AMR][1000 genomes]
rs11898394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	1.00[AMR][1000 genomes]
rs1503201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	1.00[AMR][1000 genomes]
rs17022736	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17025339	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28641817	1.00[EUR][1000 genomes]
rs35774346	0.82[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57901413	1.00[EUR][1000 genomes]
rs58187838	1.00[AMR][1000 genomes]
rs60885334	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61712471	1.00[AMR][1000 genomes]
rs6543226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	1.00[AMR][1000 genomes]
rs6736475	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737992	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6740424	1.00[EUR][1000 genomes]
rs6743285	1.00[EUR][1000 genomes]
rs6746457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	1.00[AMR][1000 genomes]
rs72942830	1.00[AMR][1000 genomes]
rs72942834	1.00[AMR][1000 genomes]
rs72942836	1.00[AMR][1000 genomes]
rs72942856	1.00[AMR][1000 genomes]
rs72942862	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942871	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.82[AFR][1000 genomes]
rs72942896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.90[AFR][1000 genomes]
rs72944825	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	1.00[AMR][1000 genomes]
rs72946417	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946421	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	1.00[AMR][1000 genomes]
rs72946448	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946453	1.00[AMR][1000 genomes]
rs7579764	1.00[AMR][1000 genomes]
rs9308889	1.00[AMR][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	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:98567600-98586600	Weak transcription	Fetal Stomach	stomach
3	chr2:98568000-98583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:98568400-98586600	Weak transcription	Aorta	Aorta
6	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:98571000-98586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:98574400-98586200	Weak transcription	NH-A	brain
9	chr2:98574600-98582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:98574600-98583200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:98574600-98583400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:98574800-98585200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:98574800-98586200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:98575000-98583000	Weak transcription	Gastric	stomach
15	chr2:98575000-98585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:98575000-98586800	Weak transcription	Brain Angular Gyrus	brain
17	chr2:98575000-98589000	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:98575200-98583000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:98575200-98583200	Weak transcription	Small Intestine	intestine
20	chr2:98575200-98584400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:98575400-98583200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:98575400-98583400	Weak transcription	Spleen	Spleen
24	chr2:98575400-98585000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:98575400-98595000	Weak transcription	HSMM	muscle
26	chr2:98575600-98586600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:98575600-98586600	Weak transcription	Lung	lung
28	chr2:98575800-98582600	Weak transcription	Right Atrium	heart
29	chr2:98575800-98587600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:98576000-98584400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:98578200-98584200	Weak transcription	Brain Substantia Nigra	brain
32	chr2:98578400-98584200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:98578400-98586600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:98578400-98587200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:98579600-98583000	Weak transcription	Fetal Lung	lung
36	chr2:98579600-98583200	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:98579600-98584200	Weak transcription	Primary T cells from cord blood	blood
38	chr2:98579600-98584200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:98579800-98582600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:98579800-98583200	Weak transcription	A549	lung
41	chr2:98580000-98582600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr2:98580000-98582800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:98580000-98582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:98580000-98589800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:98580200-98582800	Weak transcription	GM12878-XiMat	blood
46	chr2:98580200-98583600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:98580200-98584400	Weak transcription	Esophagus	oesophagus
48	chr2:98580600-98583400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr2:98580600-98583800	Enhancers	Fetal Intestine Small	intestine
50	chr2:98580800-98583000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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