Variant report

Variant	rs2857766
Chromosome Location	chr6:29634003-29634004
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr6:29633957-29634471	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:29633927-29634033	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29633969-29634019	Caco-2	colon:	n/a
2	chr6:29633969-29634019	MCF-7	breast:	n/a
3	chr6:29633971-29634021	GM06990	blood:	n/a
4	chr6:29633969-29634019	PrEC	prostate:	n/a
5	chr6:29633969-29634019	CMK	blood:	n/a
6	chr6:29633969-29634019	HEK293	kidney:	embryo
7	chr6:29633969-29634019	SKMC	muscle:	n/a
8	chr6:29633969-29634019	AG04450	lung:	fetal
9	chr6:29633971-29634021	MCF10A-Er-Src	breast:	n/a
10	chr6:29633969-29634019	GM12878	blood:	n/a
11	chr6:29633969-29634019	HAEpiC	amniotic membrane:	n/a
12	chr6:29633969-29634019	LNCaP	prostate:	n/a
13	chr6:29633969-29634019	ovcar-3	ovarian:	n/a
14	chr6:29633969-29634019	HPAEpiC	pulmonary alveolar:	n/a
15	chr6:29633969-29634019	K562	blood:	n/a
16	chr6:29633969-29634019	ECC-1	luminal epithelium:	n/a
17	chr6:29633969-29634019	GM06990	blood:	n/a
18	chr6:29633971-29634021	GM19239	blood:	n/a
19	chr6:29633969-29634019	HCPEpiC	choroid plexus:	n/a
20	chr6:29633969-29634019	NB4	blood:	n/a
21	chr6:29633969-29634019	HL-60	blood:	n/a
22	chr6:29633971-29634021	HCM	heart:	n/a
23	chr6:29633969-29634019	GM12891	blood:	n/a
24	chr6:29633969-29634019	H1-hESC	embryonic stem cell:	embryo
25	chr6:29633969-29634019	HepG2	liver:	n/a
26	chr6:29633969-29634019	PFSK-1	brain:	n/a
27	chr6:29633969-29634019	HIPEpiC	eye:	n/a
28	chr6:29633971-29634021	NHDF-neo	bronchial:	n/a
29	chr6:29633971-29634021	HUVEC	blood vessel:	n/a
30	chr6:29633969-29634019	MCF10A-Er-Src	breast:	n/a
31	chr6:29633969-29634019	HCF	heart:	n/a
32	chr6:29633969-29634019	NHDF-neo	bronchial:	n/a
33	chr6:29633971-29634021	HPAEpiC	pulmonary alveolar:	n/a
34	chr6:29633971-29634021	Caco-2	colon:	n/a
35	chr6:29633971-29634021	IMR90	lung:	fetal
36	chr6:29633969-29634019	NHBE	bronchial:	n/a
37	chr6:29633969-29634019	BE2_C	brain:	n/a
38	chr6:29633971-29634021	BJ	skin:	n/a
39	chr6:29633969-29634019	HRPEpiC	eye:	n/a
40	chr6:29633969-29634019	Hepatocyte	liver:	n/a
41	chr6:29633969-29634019	U87	brain:	n/a
42	chr6:29633971-29634021	AG09309	skin:	n/a
43	chr6:29633971-29634021	U87	brain:	n/a
44	chr6:29633971-29634021	T-47D	breast:	n/a
45	chr6:29633971-29634021	MCF-7	breast:	n/a
46	chr6:29633971-29634021	Jurkat	blood:	n/a
47	chr6:29633971-29634021	RPTEC	kidney:	n/a
48	chr6:29633971-29634021	HRCEpiC	kidney:	n/a
49	chr6:29633969-29634019	T-47D	breast:	n/a
50	chr6:29633971-29634021	ProgFib	skin:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:29619372..29622160-chr6:29632758..29634460,2	K562	blood:
2	chr6:29634001..29636635-chr6:29639490..29642126,2	K562	blood:
3	chr6:29633426..29635000-chr6:29636787..29639241,2	MCF-7	breast:

No data

Variant related genes	Relation type
MOG	TF binding region
MOG	CpG island
ENSG00000204655	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1233373	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233375	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233378	1.00[AFR][1000 genomes]
rs12661228	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12661266	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1318631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17184549	0.95[EUR][1000 genomes]
rs17369215	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17435027	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17875376	0.86[EUR][1000 genomes]
rs2252711	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256266	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857781	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34260811	0.80[EUR][1000 genomes]
rs34387568	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34912326	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35471702	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4084764	0.84[EUR][1000 genomes]
rs4391284	0.96[EUR][1000 genomes]
rs4713230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713232	0.89[AFR][1000 genomes]
rs4713233	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713237	0.83[EUR][1000 genomes]
rs4713239	0.83[EUR][1000 genomes]
rs4713240	0.83[EUR][1000 genomes]
rs4959123	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754067	0.86[EUR][1000 genomes]
rs9368609	0.83[EUR][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
rs2857766	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29629800-29634400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:29630800-29634200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:29631400-29640200	Weak transcription	NHEK	skin
6	chr6:29631800-29635200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:29632000-29634600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:29632000-29636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:29632000-29638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:29632600-29634400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:29633400-29634200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:29633400-29634400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:29633400-29634600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:29633400-29634600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:29633400-29635200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:29633400-29635600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:29633400-29635600	Genic enhancers	Brain Substantia Nigra	brain
18	chr6:29633400-29636000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:29633400-29636400	Enhancers	Fetal Heart	heart
20	chr6:29633600-29634200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:29633600-29634400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr6:29633600-29634600	Genic enhancers	Brain Angular Gyrus	brain
23	chr6:29633600-29634600	Enhancers	Brain Anterior Caudate	brain
24	chr6:29633600-29635000	Genic enhancers	Brain Cingulate Gyrus	brain
25	chr6:29633600-29635000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:29633600-29635400	Genic enhancers	Brain Hippocampus Middle	brain
27	chr6:29633600-29636600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:29633800-29634600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:29633800-29634800	Enhancers	GM12878-XiMat	blood
30	chr6:29633800-29635000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr6:29633800-29635000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr6:29633800-29635800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:29633800-29636600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr6:29634000-29636200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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