Variant report

Variant	rs2508740
Chromosome Location	chr11:76227182-76227183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:76156368..76158164-chr11:76225916..76228340,2	K562	blood:

Variant related genes	Relation type
ENSG00000158636	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10160382	0.93[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs1044265	0.81[ASW][hapmap]
rs10793167	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs10793169	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10793171	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10899217	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899222	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899225	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10899227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236749	0.84[EUR][1000 genomes]
rs11236752	0.89[EUR][1000 genomes]
rs11606394	0.81[ASW][hapmap]
rs17749618	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs1939467	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs1939468	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs2282611	0.81[GIH][hapmap]
rs2508741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508753	0.85[AMR][1000 genomes]
rs2508755	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2508756	0.81[ASW][hapmap]
rs2508759	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2508760	0.81[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508761	0.87[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508762	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513504	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2513505	0.88[AMR][1000 genomes]
rs2513508	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2513513	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2513520	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513523	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2513525	0.81[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3753051	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs3814711	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245443	0.87[ASW][hapmap];0.92[CEU][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4272809	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4300410	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4945090	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5023625	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6592635	0.82[EUR][1000 genomes]
rs7106564	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7107058	0.81[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs7109548	0.83[EUR][1000 genomes]
rs7123361	0.88[CEU][hapmap]
rs7125552	0.85[CEU][hapmap]
rs7926009	0.81[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7942257	0.81[CEU][hapmap]
rs7949258	0.85[CEU][hapmap]
rs8848	0.87[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2508740	ARHGEF17	cis	cerebellum	SCAN
rs2508740	ALG8	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76168800-76234800	Weak transcription	Psoas Muscle	Psoas
2	chr11:76184400-76235000	Weak transcription	NHEK	skin
3	chr11:76189000-76231400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr11:76190800-76234200	Weak transcription	Left Ventricle	heart
5	chr11:76191400-76239000	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:76191600-76231600	Weak transcription	NHDF-Ad	bronchial
7	chr11:76192800-76242800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:76205200-76234200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:76205200-76235800	Weak transcription	NHLF	lung
10	chr11:76205200-76254400	Weak transcription	Aorta	Aorta
11	chr11:76205400-76235800	Weak transcription	Lung	lung
12	chr11:76205400-76240000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:76205400-76254600	Weak transcription	Right Ventricle	heart
14	chr11:76205400-76255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:76205600-76239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:76205800-76235800	Weak transcription	Esophagus	oesophagus
17	chr11:76206000-76249200	Weak transcription	Colonic Mucosa	Colon
18	chr11:76207400-76239400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:76207400-76240000	Weak transcription	Brain Substantia Nigra	brain
20	chr11:76207400-76254400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:76207600-76239400	Weak transcription	Brain Angular Gyrus	brain
22	chr11:76208000-76234200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:76208000-76234200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:76208000-76235200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:76208200-76234200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:76208400-76234200	Weak transcription	Brain Anterior Caudate	brain
27	chr11:76211200-76232400	Weak transcription	Fetal Stomach	stomach
28	chr11:76212000-76234200	Weak transcription	Thymus	Thymus
29	chr11:76212000-76234400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:76212000-76235200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:76212000-76235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:76212200-76229200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:76212200-76234200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:76212400-76228200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:76212600-76234200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:76212800-76227800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:76212800-76230600	Weak transcription	Fetal Kidney	kidney
38	chr11:76212800-76235000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:76213000-76227800	Weak transcription	HSMM	muscle
40	chr11:76213000-76229200	Weak transcription	Primary T cells from cord blood	blood
41	chr11:76213000-76233600	Weak transcription	HepG2	liver
42	chr11:76213000-76237200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:76213000-76254200	Weak transcription	Fetal Heart	heart
44	chr11:76213200-76234000	Weak transcription	Fetal Brain Male	brain
45	chr11:76213200-76234200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:76213200-76235200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr11:76214400-76234800	Weak transcription	Fetal Intestine Small	intestine
48	chr11:76215800-76234200	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:76216200-76228600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:76216800-76229200	Weak transcription	Fetal Muscle Trunk	muscle

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