Variant report

Variant	rs17300022
Chromosome Location	chr7:2808517-2808518
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	chr7:2804001..2805527-chr7:2808218..2810356,2	K562	blood:
2	chr7:2799476..2802283-chr7:2806831..2808723,2	K562	blood:

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11761804	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11764225	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11765386	0.93[MEX][hapmap]
rs11765492	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11765726	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs11769532	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11772508	0.83[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs11971014	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12540539	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs17132594	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17132624	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17132665	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17132741	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs17132744	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17241904	0.84[AMR][1000 genomes]
rs55726557	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55767077	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55776032	0.86[EUR][1000 genomes]
rs55832916	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56007918	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56208415	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56356906	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56399783	0.86[EUR][1000 genomes]
rs6461600	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6964740	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6967664	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73033403	0.81[AMR][1000 genomes]
rs73047343	0.82[EUR][1000 genomes]
rs73047355	0.80[EUR][1000 genomes]
rs73047368	0.86[EUR][1000 genomes]
rs73047387	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73047393	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73049305	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73049327	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73049331	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73049341	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73049362	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73049380	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73051415	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73051444	0.81[AMR][1000 genomes]
rs73051469	0.81[AMR][1000 genomes]
rs757788	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7803944	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7804264	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7811164	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9770108	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1032282	chr7:2789555-2820774	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17300022	GET4	cis	parietal	SCAN
rs17300022	AIMP2	cis	parietal	SCAN
rs17300022	C7orf50	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
3	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:2798000-2827400	Weak transcription	Thymus	Thymus
5	chr7:2799200-2817000	Weak transcription	Dnd41	blood
6	chr7:2799200-2827200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:2799600-2825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:2800200-2815800	Weak transcription	Liver	Liver
9	chr7:2800400-2810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:2800800-2817200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:2800800-2818200	Weak transcription	Hela-S3	cervix
12	chr7:2801000-2808600	Weak transcription	Brain Germinal Matrix	brain
13	chr7:2801000-2810200	Weak transcription	Gastric	stomach
14	chr7:2801000-2810200	Weak transcription	K562	blood
15	chr7:2801000-2811000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:2801000-2812800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:2801000-2827600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:2801000-2829600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:2801000-2831600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:2801000-2831600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:2802000-2813200	Weak transcription	HSMM	muscle
22	chr7:2802000-2813400	Weak transcription	Pancreas	Pancrea
23	chr7:2802000-2817200	Weak transcription	HSMMtube	muscle
24	chr7:2802200-2815800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:2802600-2826400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:2802800-2813200	Weak transcription	Esophagus	oesophagus
27	chr7:2803200-2808800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:2803200-2813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:2803200-2814600	Weak transcription	Fetal Brain Female	brain
30	chr7:2803200-2822600	Weak transcription	Right Ventricle	heart
31	chr7:2803400-2814200	Weak transcription	Fetal Thymus	thymus
32	chr7:2803400-2818000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:2803400-2818000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:2803400-2833400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:2803600-2811000	Weak transcription	Right Atrium	heart
36	chr7:2803600-2811200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:2803600-2811200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:2803600-2811200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:2803600-2811200	Weak transcription	A549	lung
40	chr7:2803600-2814000	Weak transcription	Brain Substantia Nigra	brain
41	chr7:2803600-2814800	Weak transcription	NHEK	skin
42	chr7:2803600-2820800	Weak transcription	Fetal Heart	heart
43	chr7:2803600-2822200	Weak transcription	HUVEC	blood vessel
44	chr7:2803600-2822600	Weak transcription	Left Ventricle	heart
45	chr7:2803600-2824200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:2803600-2826800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:2803800-2811000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:2803800-2811000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:2803800-2811000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:2803800-2811000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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