Variant report

Variant	rs2680899
Chromosome Location	chr8:59522034-59522035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:59513092..59517407-chr8:59519565..59524210,4	K562	blood:
2	chr8:59521107..59523684-chr8:59527197..59529248,2	K562	blood:
3	chr8:59510450..59512317-chr8:59520853..59522747,2	K562	blood:
4	chr8:59485344..59486960-chr8:59521397..59524305,2	K562	blood:

Variant related genes	Relation type
ENSG00000035681	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10099912	0.80[JPT][hapmap]
rs10111180	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs12334684	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12674724	0.86[ASN][1000 genomes]
rs16923594	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs17272151	0.81[GIH][hapmap]
rs2255834	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279460	0.90[JPT][hapmap]
rs2279462	0.90[JPT][hapmap]
rs2326129	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2634488	0.94[ASN][1000 genomes]
rs2634527	0.85[TSI][hapmap]
rs2634530	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2634531	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2634534	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2680897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28819228	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2946578	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4579515	0.80[JPT][hapmap]
rs4598239	0.81[GIH][hapmap]
rs4737504	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6985007	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6985643	0.85[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6987187	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6991020	0.83[ASN][1000 genomes]
rs7820921	0.94[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7825739	0.81[GIH][hapmap]
rs7836960	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7844231	0.90[JPT][hapmap]
rs901954	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv890939	chr8:59471187-59544413	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1031537	chr8:59482949-59536971	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv831325	chr8:59492580-59694443	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2680899	TOX	cis	cerebellum	SCAN
rs2680899	RAB2A	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59467400-59559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:59483800-59528000	Strong transcription	Dnd41	blood
3	chr8:59498600-59548400	Weak transcription	Stomach Mucosa	stomach
4	chr8:59500200-59524600	Weak transcription	HepG2	liver
5	chr8:59500600-59528800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr8:59503000-59545400	Weak transcription	Esophagus	oesophagus
7	chr8:59507400-59561200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr8:59507600-59524800	Weak transcription	Fetal Kidney	kidney
9	chr8:59507600-59525200	Weak transcription	Ovary	ovary
10	chr8:59507600-59545400	Weak transcription	Gastric	stomach
11	chr8:59508000-59523400	Weak transcription	Pancreas	Pancrea
12	chr8:59508000-59538800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr8:59508000-59545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:59508200-59533800	Weak transcription	Small Intestine	intestine
15	chr8:59508200-59542200	Weak transcription	Aorta	Aorta
16	chr8:59508200-59542400	Weak transcription	Psoas Muscle	Psoas
17	chr8:59509000-59524000	Strong transcription	Fetal Thymus	thymus
18	chr8:59509000-59542200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr8:59509000-59543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:59509000-59560400	Weak transcription	Brain Substantia Nigra	brain
21	chr8:59509600-59523400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr8:59509800-59542400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr8:59510000-59523600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr8:59510200-59523000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr8:59510200-59524600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr8:59510200-59526800	Weak transcription	Brain Angular Gyrus	brain
27	chr8:59510200-59527200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr8:59510200-59542400	Weak transcription	Lung	lung
29	chr8:59510200-59554800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr8:59510400-59551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:59510400-59570200	Weak transcription	Colonic Mucosa	Colon
32	chr8:59512000-59542200	Weak transcription	Right Ventricle	heart
33	chr8:59512200-59542200	Weak transcription	NH-A	brain
34	chr8:59512400-59540400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:59512600-59525000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:59512800-59527000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr8:59512800-59534600	Weak transcription	Placenta	Placenta
38	chr8:59513000-59523000	Weak transcription	NHEK	skin
39	chr8:59513000-59523200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:59513000-59533200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr8:59513000-59541600	Weak transcription	Brain Germinal Matrix	brain
42	chr8:59513000-59542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr8:59513000-59561200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr8:59514400-59523600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr8:59516000-59522800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr8:59516000-59535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr8:59517200-59522200	Strong transcription	Fetal Intestine Small	intestine
48	chr8:59517600-59523200	Weak transcription	Left Ventricle	heart
49	chr8:59517800-59525200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:59518400-59522400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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