Variant report

Variant	rs6925339
Chromosome Location	chr6:109559416-109559417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109556893..109560362-chr6:109702019..109704753,3	K562	blood:
2	chr6:109555640..109560553-chr6:109624000..109628580,4	K562	blood:
3	chr6:109554938..109560362-chr6:109702019..109707132,8	K562	blood:

Variant related genes	Relation type
ENSG00000201023	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11153161	0.95[ASN][1000 genomes]
rs11153165	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs11153166	0.91[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs11153167	0.91[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs11153168	0.84[CEU][hapmap]
rs11964178	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11966072	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs12664455	0.82[EUR][1000 genomes]
rs1271693	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13196219	0.87[CEU][hapmap]
rs13196590	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs13200047	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs13202939	0.82[TSI][hapmap]
rs13211313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13211944	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1741923	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34774766	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351716	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351717	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351718	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351719	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351720	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351721	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351722	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351723	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351724	0.80[CEU][hapmap]
rs351725	0.80[CEU][hapmap]
rs351726	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351727	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351728	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs351730	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351731	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351732	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351735	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351744	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351746	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351747	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351750	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351751	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353052	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs377436	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs388526	0.95[ASN][1000 genomes]
rs396635	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs408944	0.96[ASN][1000 genomes]
rs410449	0.95[ASN][1000 genomes]
rs412754	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs418093	0.93[ASN][1000 genomes]
rs421790	0.95[ASN][1000 genomes]
rs422113	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429534	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301336	0.82[TSI][hapmap]
rs436880	0.96[ASN][1000 genomes]
rs4427037	0.84[CEU][hapmap]
rs446974	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448496	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs449736	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4548045	0.90[EUR][1000 genomes]
rs55677234	0.88[EUR][1000 genomes]
rs566164	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59673	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6919423	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7773490	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs830552	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830554	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830556	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320278	0.99[ASN][1000 genomes]
rs9374069	0.83[CEU][hapmap]
rs9374070	0.84[CEU][hapmap]
rs9374071	0.84[CEU][hapmap]
rs9374072	0.83[CEU][hapmap]
rs9374076	0.88[EUR][1000 genomes]
rs9374081	0.87[CEU][hapmap]
rs9384701	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9384703	0.83[CEU][hapmap]
rs9384704	0.80[CEU][hapmap]
rs9386774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9386775	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9386779	0.85[EUR][1000 genomes]
rs9386781	0.83[CEU][hapmap]
rs9386784	0.83[CEU][hapmap]
rs9398191	0.84[CEU][hapmap]
rs9398192	0.84[CEU][hapmap]
rs9400265	0.88[EUR][1000 genomes]
rs9487049	0.87[EUR][1000 genomes]
rs949881	0.84[CEU][hapmap]
rs949882	0.84[CEU][hapmap]

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	nsv527657	chr6:109533385-109579675	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6925339	ATG5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109556800-109562800	Enhancers	Primary hematopoietic stem cells	blood
2	chr6:109556800-109564200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:109557000-109560600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:109557200-109562000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:109557200-109565000	Enhancers	NHDF-Ad	bronchial
6	chr6:109557400-109562000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:109557400-109562200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:109557600-109559600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr6:109557600-109562000	Enhancers	Stomach Mucosa	stomach
10	chr6:109557600-109565200	Enhancers	Hela-S3	cervix
11	chr6:109558000-109560000	Weak transcription	Right Atrium	heart
12	chr6:109558000-109560200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:109558000-109562000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:109558200-109559800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:109558200-109560000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:109558200-109560400	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:109558200-109560400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:109558200-109565000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:109558200-109565200	Enhancers	Osteobl	bone
20	chr6:109558200-109572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:109558400-109560200	Weak transcription	HepG2	liver
22	chr6:109558400-109560400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:109558400-109560400	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:109558400-109561400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:109558600-109559600	Weak transcription	Adipose Nuclei	Adipose
26	chr6:109558600-109560000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:109558600-109561800	Weak transcription	HSMMtube	muscle
28	chr6:109558600-109562800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:109558800-109566400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:109559000-109560000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:109559000-109560400	Weak transcription	HSMM	muscle
32	chr6:109559000-109563400	Enhancers	Primary B cells from cord blood	blood
33	chr6:109559000-109564000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:109559000-109564200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:109559200-109560400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr6:109559200-109561600	Weak transcription	Fetal Thymus	thymus
37	chr6:109559200-109564200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:109559400-109560000	Weak transcription	Brain Angular Gyrus	brain
39	chr6:109559400-109560400	Weak transcription	Lung	lung
40	chr6:109559400-109560400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:109559400-109561200	Enhancers	K562	blood
42	chr6:109559400-109561600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:109559400-109561600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:109559400-109561600	Weak transcription	Placenta	Placenta
45	chr6:109559400-109561600	Weak transcription	Spleen	Spleen
46	chr6:109559400-109563600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr6:109559400-109563600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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