Variant report

Variant	rs2071789
Chromosome Location	chr6:28912076-28912077
allele	A/G
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28583985..28585633-chr6:28910730..28913227,2	K562	blood:
4	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
5	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
6	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf100-11	chr6:28911561-28912315	NONHSAT108497

No data

Variant related genes	Relation type
ENSG00000263426	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs9257260	0.82[EUR][1000 genomes]
rs9257316	0.81[EUR][1000 genomes]
rs9257319	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9257438	0.80[AMR][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	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071789	PGBD1	cis	cerebellum	SCAN
rs2071789	HIST1H2AE	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907400-28912400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28907400-28912400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28907400-28912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:28907400-28912400	Active TSS	A549	lung
6	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:28907800-28912400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:28907800-28912400	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:28910200-28912400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:28910200-28912400	Active TSS	Brain Angular Gyrus	brain
12	chr6:28910600-28912400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:28911000-28912200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:28911000-28912200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr6:28911000-28912200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr6:28911000-28912400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:28911000-28912400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:28911000-28912400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:28911000-28912400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:28911000-28912400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:28911000-28912400	Active TSS	Brain Substantia Nigra	brain
22	chr6:28911000-28912400	Active TSS	Colon Smooth Muscle	Colon
23	chr6:28911000-28912400	Active TSS	Right Ventricle	heart
24	chr6:28911000-28912600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28911000-28912600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:28911000-28912600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:28911000-28912600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr6:28911000-28912600	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr6:28911000-28912600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:28911000-28912800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:28911200-28912200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:28911200-28912200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr6:28911200-28912200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr6:28911200-28912200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:28911200-28912200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr6:28911200-28912200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:28911200-28912200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:28911200-28912200	Flanking Active TSS	Liver	Liver
39	chr6:28911200-28912200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr6:28911200-28912200	Active TSS	Small Intestine	intestine
41	chr6:28911200-28912400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr6:28911200-28912400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:28911200-28912400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:28911200-28912400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:28911200-28912400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr6:28911200-28912400	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr6:28911200-28912400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr6:28911200-28912400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:28911200-28912400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:28911200-28912400	Active TSS	Muscle Satellite Cultured Cells	--

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