Variant report

Variant	rs4870537
Chromosome Location	chr6:150939368-150939369
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150933927..150936291-chr6:150938696..150941603,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11968779	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1352975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17080012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs201531	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2345668	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2345669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs275348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4323318	1.00[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4400227	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4530869	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4869921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869924	1.00[JPT][hapmap]
rs4869932	1.00[JPT][hapmap]
rs4870533	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870534	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62432653	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432656	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432657	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432658	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432659	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434061	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434062	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434064	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434092	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434093	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434094	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434095	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434096	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434097	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434098	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434099	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434100	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434101	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434102	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434103	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62434104	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73002187	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73002188	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73002195	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73004311	0.93[EUR][1000 genomes]
rs73016045	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73016054	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9478767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478768	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9478772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9478773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9478774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9478777	1.00[JPT][hapmap]
rs9480490	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9480493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480499	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9480503	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9480505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9480511	1.00[JPT][hapmap]
rs9480516	1.00[JPT][hapmap]
rs9480517	1.00[JPT][hapmap]
rs9480518	1.00[JPT][hapmap]
rs9480521	1.00[JPT][hapmap]
rs9480522	1.00[JPT][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	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv464080	chr6:150923115-150941310	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
3	nsv604851	chr6:150923115-150941310	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv886774	chr6:150931131-150983318	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4870537	RAET1E	cis	cerebellum	SCAN
rs4870537	IYD	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150922400-150941400	Weak transcription	Colonic Mucosa	Colon
2	chr6:150928200-150944800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:150928400-150939600	Weak transcription	Brain Angular Gyrus	brain
4	chr6:150928400-150940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:150928400-150952800	Weak transcription	Right Ventricle	heart
6	chr6:150928600-150948800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:150929400-150941400	Weak transcription	Fetal Stomach	stomach
8	chr6:150931000-150947400	Weak transcription	Placenta	Placenta
9	chr6:150934200-150940000	Weak transcription	Left Ventricle	heart
10	chr6:150935000-150943800	Weak transcription	Liver	Liver
11	chr6:150935800-150940200	Weak transcription	Lung	lung
12	chr6:150936600-150944600	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:150937000-150941400	Enhancers	Thymus	Thymus
14	chr6:150937600-150940400	Enhancers	Fetal Thymus	thymus
15	chr6:150937600-150941400	Enhancers	Primary B cells from cord blood	blood
16	chr6:150938000-150941000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:150938200-150939600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:150938400-150939600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:150938400-150939800	Enhancers	Fetal Lung	lung
20	chr6:150938600-150939600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:150938600-150939600	Enhancers	Fetal Kidney	kidney
22	chr6:150938600-150939800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:150938600-150939800	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:150938600-150941400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:150938600-150941800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:150938600-150942000	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:150938600-150942400	Enhancers	Brain Substantia Nigra	brain
28	chr6:150938600-150943800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:150938800-150939600	Enhancers	Brain Hippocampus Middle	brain
30	chr6:150938800-150939800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:150938800-150941400	Weak transcription	Stomach Mucosa	stomach
32	chr6:150938800-150942000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:150939000-150939600	Enhancers	Small Intestine	intestine
34	chr6:150939000-150940200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:150939000-150940400	Weak transcription	Brain Anterior Caudate	brain
36	chr6:150939000-150944600	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:150939000-150945200	Enhancers	Adipose Nuclei	Adipose
38	chr6:150939000-150949600	Weak transcription	Pancreas	Pancrea
39	chr6:150939000-150954200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:150939200-150939600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:150939200-150940200	Weak transcription	Right Atrium	heart
42	chr6:150939200-150940200	Weak transcription	Spleen	Spleen
43	chr6:150939200-150940800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:150939200-150941400	Weak transcription	Fetal Intestine Small	intestine
45	chr6:150939200-150941400	Weak transcription	Gastric	stomach
46	chr6:150939200-150942400	Enhancers	HUVEC	blood vessel
47	chr6:150939200-150944600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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