Variant report

Variant	rs9468571
Chromosome Location	chr6:29624894-29624895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29624846-29624896	U87	brain:	n/a
2	chr6:29624846-29624896	K562	blood:	n/a
3	chr6:29624846-29624896	HNPCEpiC	eye:	n/a
4	chr6:29624846-29624896	BJ	skin:	n/a
5	chr6:29624846-29624896	IMR90	lung:	fetal
6	chr6:29624846-29624896	Caco-2	colon:	n/a
7	chr6:29624846-29624896	HEEpiC	esophagus:	n/a
8	chr6:29624846-29624896	AG09319	gingival:	n/a
9	chr6:29624846-29624896	PrEC	prostate:	n/a
10	chr6:29624846-29624896	AoSMC	blood vessel:	n/a
11	chr6:29624846-29624896	AG04449	skin:	fetal
12	chr6:29624846-29624896	ovcar-3	ovarian:	n/a
13	chr6:29624846-29624896	HRPEpiC	eye:	n/a
14	chr6:29624846-29624896	HCM	heart:	n/a
15	chr6:29624846-29624896	A549	lung:	n/a
16	chr6:29624846-29624896	SAEC	small airway:	n/a
17	chr6:29624846-29624896	Hela-S3	cervix:	n/a
18	chr6:29624846-29624896	GM06990	blood:	n/a
19	chr6:29624846-29624896	AG10803	skin:	n/a
20	chr6:29624846-29624896	T-47D	breast:	n/a
21	chr6:29624846-29624896	MCF10A-Er-Src	breast:	n/a
22	chr6:29624846-29624896	HCT-116	colon:	n/a
23	chr6:29624846-29624896	GM12891	blood:	n/a
24	chr6:29624846-29624896	NB4	blood:	n/a
25	chr6:29624846-29624896	NT2-D1	testis:	n/a
26	chr6:29624846-29624896	PFSK-1	brain:	n/a
27	chr6:29624846-29624896	GM19239	blood:	n/a
28	chr6:29624846-29624896	NHDF-neo	bronchial:	n/a
29	chr6:29624846-29624896	GM12878	blood:	n/a
30	chr6:29624846-29624896	AG09309	skin:	n/a
31	chr6:29624846-29624896	SK-N-SH	brain:	n/a
32	chr6:29624846-29624896	RPTEC	kidney:	n/a
33	chr6:29624846-29624896	GM12892	blood:	n/a
34	chr6:29624846-29624896	CMK	blood:	n/a
35	chr6:29624846-29624896	H1-hESC	embryonic stem cell:	embryo
36	chr6:29624846-29624896	NH-A	brain:	n/a
37	chr6:29624846-29624896	PANC-1	pancreas:	n/a
38	chr6:29624846-29624896	HIPEpiC	eye:	n/a
39	chr6:29624846-29624896	MCF-7	breast:	n/a
40	chr6:29624846-29624896	SK-N-MC	brain:	n/a
41	chr6:29624846-29624896	LNCaP	prostate:	n/a
42	chr6:29624846-29624896	HepG2	liver:	n/a
43	chr6:29624846-29624896	NHBE	bronchial:	n/a
44	chr6:29624846-29624896	Jurkat	blood:	n/a
45	chr6:29624846-29624896	ProgFib	skin:	n/a
46	chr6:29624846-29624896	SK-N-SH_RA	brain:	n/a
47	chr6:29624846-29624896	HRCEpiC	kidney:	n/a
48	chr6:29624846-29624896	HL-60	blood:	n/a
49	chr6:29624846-29624896	HRE	kidney:	n/a
50	chr6:29624846-29624896	HAEpiC	amniotic membrane:	n/a

No data

Variant related genes	Relation type
MOG	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17178518	0.86[ASN][1000 genomes]
rs17178532	0.86[ASN][1000 genomes]
rs29234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29235	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29238	0.86[ASN][1000 genomes]
rs29240	0.86[ASN][1000 genomes]
rs29272	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025623	0.86[ASN][1000 genomes]
rs3909134	0.86[ASN][1000 genomes]
rs73747624	0.86[ASN][1000 genomes]
rs9461541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500947	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468571	HLA-A	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29618400-29629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:29618400-29629600	Weak transcription	Right Ventricle	heart
3	chr6:29620000-29628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:29620000-29631200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:29620600-29626600	Enhancers	Fetal Heart	heart
6	chr6:29621000-29625000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:29621800-29625000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:29622800-29625000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:29623200-29625200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:29623400-29625000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:29623400-29630600	Active TSS	Brain Anterior Caudate	brain
12	chr6:29623600-29627200	Active TSS	Brain Hippocampus Middle	brain
13	chr6:29623800-29625000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:29624000-29625000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:29624000-29628000	Active TSS	Brain Angular Gyrus	brain
16	chr6:29624200-29625000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:29624200-29627800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:29624200-29628000	Active TSS	Brain Cingulate Gyrus	brain
19	chr6:29624200-29628000	Active TSS	Brain Substantia Nigra	brain
20	chr6:29624400-29625200	Enhancers	GM12878-XiMat	blood
21	chr6:29624400-29629200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr6:29624400-29630400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:29624600-29625000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:29624600-29625000	Enhancers	Left Ventricle	heart
25	chr6:29624600-29625200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:29624600-29628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:29624600-29628600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:29624800-29625000	Bivalent Enhancer	Lung	lung
29	chr6:29624800-29625000	Genic enhancers	Right Atrium	heart
30	chr6:29624800-29628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:29624800-29628800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:29624800-29629000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:29624800-29631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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