Variant report

Variant	rs29272
Chromosome Location	chr6:29618366-29618367
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:29593421..29596019-chr6:29617479..29619432,2	K562	blood:
2	chr6:29608179..29610477-chr6:29617988..29619609,2	K562	blood:
3	chr6:29598640..29604637-chr6:29614654..29620933,9	K562	blood:
4	chr6:29608179..29609839-chr6:29617502..29619488,2	K562	blood:
5	chr6:29616642..29621245-chr6:29621568..29627231,6	K562	blood:
6	chr6:29617940..29618834-chr6:29653305..29654103,4	MCF-7	breast:
7	chr6:29593197..29596046-chr6:29616000..29618979,4	K562	blood:
8	chr6:29617916..29618459-chr6:29653660..29654518,2	MCF-7	breast:
9	chr6:29615912..29617460-chr6:29617899..29619662,2	MCF-7	breast:
10	chr6:29598560..29601918-chr6:29614006..29619393,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction
ENSG00000204655	Chromatin interaction
ENSG00000235238	Chromatin interaction

Extended variants
information (count: 16 )
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];0.97[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]
rs3025623	0.86[ASN][1000 genomes]
rs3909134	0.86[ASN][1000 genomes]
rs73747624	0.86[ASN][1000 genomes]
rs9461541	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468571	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468572	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500947	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv527037	chr6:29615822-29624112	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29272	HLA-A	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29616400-29618600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:29617200-29618400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:29617200-29618400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr6:29617200-29618400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:29617200-29618400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:29617200-29618400	Active TSS	A549	lung
7	chr6:29617200-29618400	Flanking Active TSS	HMEC	breast
8	chr6:29617200-29618400	Flanking Active TSS	NHEK	skin
9	chr6:29617400-29618400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:29617400-29618400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:29617400-29618400	Enhancers	Fetal Heart	heart
12	chr6:29617400-29618400	Flanking Active TSS	Hela-S3	cervix
13	chr6:29617400-29618400	Flanking Active TSS	HUVEC	blood vessel
14	chr6:29617400-29618400	Flanking Active TSS	K562	blood
15	chr6:29617400-29618400	Active TSS	NHLF	lung
16	chr6:29617600-29618400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:29617600-29618400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:29617600-29618400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:29617600-29618400	Active TSS	Fetal Brain Male	brain
20	chr6:29617600-29618400	Active TSS	Fetal Brain Female	brain
21	chr6:29617600-29618400	Flanking Active TSS	NH-A	brain
22	chr6:29617800-29618400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:29617800-29619600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:29617800-29622800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:29618000-29618400	Enhancers	H9 Cell Line	embryonic stem cell
26	chr6:29618000-29618400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:29618000-29618400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr6:29618000-29618400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr6:29618000-29618400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:29618000-29618400	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr6:29618000-29618400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:29618000-29618400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:29618000-29618400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr6:29618000-29618400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:29618000-29618400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:29618000-29618400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr6:29618000-29618400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:29618000-29618400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:29618000-29618400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:29618000-29618400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:29618000-29618400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:29618000-29618400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:29618000-29618400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr6:29618000-29618400	Enhancers	Liver	Liver
45	chr6:29618000-29618400	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr6:29618000-29618400	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr6:29618000-29618400	Enhancers	Brain Germinal Matrix	brain
48	chr6:29618000-29618400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr6:29618000-29618400	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr6:29618000-29618400	Flanking Active TSS	Duodenum Mucosa	Duodenum

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