Variant report

Variant	rs2634533
Chromosome Location	chr8:59535622-59535623
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17273109	0.82[AFR][1000 genomes]
rs2326078	0.89[AMR][1000 genomes]
rs2634529	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634532	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680896	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680898	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680900	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680903	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2680904	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2969915	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4307329	0.89[AMR][1000 genomes]
rs6995690	0.94[AMR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2634533	CCL3L1	trans	brain	seeQTL
rs2634533	EGR2	trans	brain	seeQTL
rs2634533	PTGS2	trans	brain	seeQTL
rs2634533	CCL3	trans	brain	seeQTL
rs2634533	CCL4	trans	brain	seeQTL

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	chr8:59508200-59542200	Weak transcription	Aorta	Aorta
9	chr8:59508200-59542400	Weak transcription	Psoas Muscle	Psoas
10	chr8:59509000-59542200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr8:59509000-59543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:59509000-59560400	Weak transcription	Brain Substantia Nigra	brain
13	chr8:59509800-59542400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:59510200-59542400	Weak transcription	Lung	lung
15	chr8:59510200-59554800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr8:59510400-59551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr8:59510400-59570200	Weak transcription	Colonic Mucosa	Colon
18	chr8:59512000-59542200	Weak transcription	Right Ventricle	heart
19	chr8:59512200-59542200	Weak transcription	NH-A	brain
20	chr8:59512400-59540400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:59513000-59541600	Weak transcription	Brain Germinal Matrix	brain
22	chr8:59513000-59542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr8:59513000-59561200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr8:59520200-59542200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr8:59520600-59541600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr8:59520600-59554600	Weak transcription	HMEC	breast
27	chr8:59521000-59542800	Weak transcription	Hela-S3	cervix
28	chr8:59521800-59542200	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:59521800-59542400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr8:59521800-59542400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr8:59522000-59570200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr8:59522200-59537400	Weak transcription	A549	lung
33	chr8:59522200-59538800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr8:59522200-59541400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:59522200-59542400	Weak transcription	HUVEC	blood vessel
36	chr8:59522200-59542800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr8:59522200-59545200	Weak transcription	Spleen	Spleen
38	chr8:59522400-59537200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr8:59522400-59541800	Weak transcription	NHLF	lung
40	chr8:59524000-59542400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:59524200-59554400	Weak transcription	NHEK	skin
42	chr8:59525200-59542200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr8:59525400-59541000	Weak transcription	HepG2	liver
44	chr8:59526600-59542400	Weak transcription	Fetal Heart	heart
45	chr8:59527200-59542200	Weak transcription	Brain Angular Gyrus	brain
46	chr8:59527400-59542200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr8:59529000-59537600	Weak transcription	Primary B cells from cord blood	blood
48	chr8:59529200-59542600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr8:59529400-59554600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr8:59529600-59543000	Weak transcription	HSMM	muscle

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