Variant report

Variant	rs4598239
Chromosome Location	chr8:59532707-59532708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:59531274..59532997-chr8:59558772..59560401,2	K562	blood:
2	chr8:59531187..59532798-chr8:59569997..59572188,2	MCF-7	breast:
3	chr8:59530465..59533634-chr8:59535645..59538815,3	K562	blood:

Variant related genes	Relation type
ENSG00000035681	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10087843	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10088541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090212	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10090837	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10091952	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10111180	1.00[ASW][hapmap]
rs10112330	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10113323	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10113830	0.97[ASN][1000 genomes]
rs1050504	0.84[TSI][hapmap]
rs10957063	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11774998	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11985566	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11994921	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171670	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12679938	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs1352496	0.97[ASN][1000 genomes]
rs1387222	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16923637	0.84[ASN][1000 genomes]
rs17206746	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17272151	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2130072	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255834	0.83[GIH][hapmap]
rs2326129	0.88[EUR][1000 genomes]
rs2680899	0.81[GIH][hapmap]
rs28429099	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28489122	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28755983	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28886919	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816846	0.84[TSI][hapmap]
rs4266636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60567264	0.85[ASN][1000 genomes]
rs6471732	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6985643	0.84[GIH][hapmap]
rs6998210	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7006937	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7011066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72647451	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7820921	0.82[GIH][hapmap]
rs7825739	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]
rs7833791	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs4598239	MOS	cis	parietal	SCAN
rs4598239	RAB2A	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr8:59498600-59548400	Weak transcription	Stomach Mucosa	stomach
3	chr8:59503000-59545400	Weak transcription	Esophagus	oesophagus
4	chr8:59507400-59561200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr8:59507600-59545400	Weak transcription	Gastric	stomach
6	chr8:59508000-59538800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:59508000-59545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:59508200-59533800	Weak transcription	Small Intestine	intestine
9	chr8:59508200-59542200	Weak transcription	Aorta	Aorta
10	chr8:59508200-59542400	Weak transcription	Psoas Muscle	Psoas
11	chr8:59509000-59542200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr8:59509000-59543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:59509000-59560400	Weak transcription	Brain Substantia Nigra	brain
14	chr8:59509800-59542400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr8:59510200-59542400	Weak transcription	Lung	lung
16	chr8:59510200-59554800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr8:59510400-59551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr8:59510400-59570200	Weak transcription	Colonic Mucosa	Colon
19	chr8:59512000-59542200	Weak transcription	Right Ventricle	heart
20	chr8:59512200-59542200	Weak transcription	NH-A	brain
21	chr8:59512400-59540400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:59512800-59534600	Weak transcription	Placenta	Placenta
23	chr8:59513000-59533200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:59513000-59541600	Weak transcription	Brain Germinal Matrix	brain
25	chr8:59513000-59542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:59513000-59561200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr8:59516000-59535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr8:59520200-59535200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr8:59520200-59542200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr8:59520400-59533800	Weak transcription	Liver	Liver
31	chr8:59520400-59534600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr8:59520600-59535400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr8:59520600-59541600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr8:59520600-59554600	Weak transcription	HMEC	breast
35	chr8:59520800-59535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr8:59521000-59542800	Weak transcription	Hela-S3	cervix
37	chr8:59521200-59533800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:59521400-59533400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:59521400-59533600	Weak transcription	Fetal Lung	lung
40	chr8:59521800-59535400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr8:59521800-59542200	Weak transcription	Colon Smooth Muscle	Colon
42	chr8:59521800-59542400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:59521800-59542400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr8:59522000-59570200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr8:59522200-59533200	Weak transcription	Fetal Intestine Large	intestine
46	chr8:59522200-59533600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr8:59522200-59535400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr8:59522200-59537400	Weak transcription	A549	lung
49	chr8:59522200-59538800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr8:59522200-59541400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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