Variant report

Variant	rs7825739
Chromosome Location	chr8:59519476-59519477
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	chr8:59502026..59503771-chr8:59518248..59520928,2	K562	blood:

Variant related genes	Relation type
ENSG00000035681	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10087843	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10088541	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10090212	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10090837	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10091952	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10112330	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10113323	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10113667	0.85[ASN][1000 genomes]
rs10113830	0.86[ASN][1000 genomes]
rs1050504	0.84[TSI][hapmap]
rs10957063	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11774998	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11985566	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11994921	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12171670	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12679938	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs1352496	0.85[ASN][1000 genomes]
rs1387222	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17206746	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17272151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2130072	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2255834	0.83[GIH][hapmap]
rs2326129	0.89[EUR][1000 genomes]
rs2680899	0.81[GIH][hapmap]
rs28429099	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28489122	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28755983	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28886919	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3816846	0.84[TSI][hapmap]
rs4266636	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4598239	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471732	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6985643	0.84[GIH][hapmap]
rs6998210	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7006937	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7011066	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72647451	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7820921	0.82[GIH][hapmap]
rs7833791	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9297999	0.84[TSI][hapmap]

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
rs7825739	MOS	cis	parietal	SCAN
rs7825739	RAB2A	cis	cerebellum	SCAN

Chromatin state (count:118 , 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	chr8:59500600-59521000	Weak transcription	Fetal Heart	heart
6	chr8:59500600-59528800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:59503000-59545400	Weak transcription	Esophagus	oesophagus
8	chr8:59507400-59561200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr8:59507600-59521800	Weak transcription	Spleen	Spleen
10	chr8:59507600-59524800	Weak transcription	Fetal Kidney	kidney
11	chr8:59507600-59525200	Weak transcription	Ovary	ovary
12	chr8:59507600-59545400	Weak transcription	Gastric	stomach
13	chr8:59508000-59521000	Weak transcription	Brain Hippocampus Middle	brain
14	chr8:59508000-59523400	Weak transcription	Pancreas	Pancrea
15	chr8:59508000-59538800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:59508000-59545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:59508200-59533800	Weak transcription	Small Intestine	intestine
18	chr8:59508200-59542200	Weak transcription	Aorta	Aorta
19	chr8:59508200-59542400	Weak transcription	Psoas Muscle	Psoas
20	chr8:59508800-59521000	Weak transcription	Fetal Brain Male	brain
21	chr8:59509000-59524000	Strong transcription	Fetal Thymus	thymus
22	chr8:59509000-59542200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr8:59509000-59543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:59509000-59560400	Weak transcription	Brain Substantia Nigra	brain
25	chr8:59509600-59523400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr8:59509800-59520000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr8:59509800-59542400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr8:59510000-59519800	Weak transcription	Fetal Brain Female	brain
29	chr8:59510000-59523600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr8:59510200-59519800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr8:59510200-59523000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr8:59510200-59524600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr8:59510200-59526800	Weak transcription	Brain Angular Gyrus	brain
34	chr8:59510200-59527200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr8:59510200-59542400	Weak transcription	Lung	lung
36	chr8:59510200-59554800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr8:59510400-59551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr8:59510400-59570200	Weak transcription	Colonic Mucosa	Colon
39	chr8:59510800-59520000	Weak transcription	HMEC	breast
40	chr8:59512000-59542200	Weak transcription	Right Ventricle	heart
41	chr8:59512200-59542200	Weak transcription	NH-A	brain
42	chr8:59512400-59540400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:59512600-59519800	Weak transcription	Brain Anterior Caudate	brain
44	chr8:59512600-59525000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr8:59512800-59519600	Weak transcription	A549	lung
46	chr8:59512800-59521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr8:59512800-59527000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr8:59512800-59534600	Weak transcription	Placenta	Placenta
49	chr8:59513000-59519800	Weak transcription	Liver	Liver
50	chr8:59513000-59519800	Weak transcription	Duodenum Mucosa	Duodenum

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