Variant report

Variant	rs3807031
Chromosome Location	chr6:30033884-30033885
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:30033682-30035697	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:30033822-30034071	K562	blood:	n/a	n/a
3	POLR2A	chr6:30033687-30035386	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:30033681-30035402	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr6:30033747-30035349	GM12892	blood:	n/a	n/a
6	JUN	chr6:30033661-30035734	K562	blood:	n/a	chr6:30035268-30035277 chr6:30035265-30035274
7	POLR2A	chr6:30033875-30035161	K562	blood:	n/a	n/a
8	POLR2A	chr6:30033828-30033889	ProgFib	skin:	n/a	n/a
9	POLR2A	chr6:30033780-30035297	HCT-116	colon:	n/a	n/a
10	POLR2A	chr6:30033763-30035352	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:30033706-30034068	K562	blood:	n/a	n/a
12	POLR2A	chr6:30033738-30035539	K562	blood:	n/a	n/a
13	POLR2A	chr6:30033807-30034112	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:30033685-30035337	PFSK-1	brain:	n/a	n/a
15	MXI1	chr6:30033710-30035798	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr6:30033786-30035526	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr6:30033800-30035246	GM12891	blood:	n/a	n/a
18	POLR2A	chr6:30033807-30035564	IMR90	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30033850-30033900	SK-N-SH	brain:	n/a
2	chr6:30033850-30033900	HNPCEpiC	eye:	n/a
3	chr6:30033850-30033900	NT2-D1	testis:	n/a
4	chr6:30033850-30033900	HRE	kidney:	n/a
5	chr6:30033850-30033900	GM12878	blood:	n/a
6	chr6:30033850-30033900	NB4	blood:	n/a
7	chr6:30033850-30033900	SAEC	small airway:	n/a
8	chr6:30033850-30033900	AG04450	lung:	fetal
9	chr6:30033850-30033900	ECC-1	luminal epithelium:	n/a
10	chr6:30033850-30033900	GM19239	blood:	n/a
11	chr6:30033850-30033900	AoSMC	blood vessel:	n/a
12	chr6:30033850-30033900	HCPEpiC	choroid plexus:	n/a
13	chr6:30033850-30033900	HCF	heart:	n/a
14	chr6:30033850-30033900	SKMC	muscle:	n/a
15	chr6:30033850-30033900	HCT-116	colon:	n/a
16	chr6:30033850-30033900	AG09309	skin:	n/a
17	chr6:30033850-30033900	NHDF-neo	bronchial:	n/a
18	chr6:30033850-30033900	CMK	blood:	n/a
19	chr6:30033850-30033900	BE2_C	brain:	n/a
20	chr6:30033850-30033900	NHBE	bronchial:	n/a
21	chr6:30033850-30033900	SK-N-MC	brain:	n/a
22	chr6:30033850-30033900	AG09319	gingival:	n/a
23	chr6:30033850-30033900	MCF10A-Er-Src	breast:	n/a
24	chr6:30033850-30033900	Jurkat	blood:	n/a
25	chr6:30033850-30033900	HMEC	breast:	n/a
26	chr6:30033850-30033900	SK-N-SH_RA	brain:	n/a
27	chr6:30033850-30033900	AG10803	skin:	n/a
28	chr6:30033850-30033900	HCM	heart:	n/a
29	chr6:30033850-30033900	HIPEpiC	eye:	n/a
30	chr6:30033850-30033900	NH-A	brain:	n/a
31	chr6:30033850-30033900	AG04449	skin:	fetal
32	chr6:30033850-30033900	PFSK-1	brain:	n/a
33	chr6:30033850-30033900	Hepatocyte	liver:	n/a
34	chr6:30033850-30033900	HepG2	liver:	n/a
35	chr6:30033850-30033900	HRPEpiC	eye:	n/a
36	chr6:30033850-30033900	BJ	skin:	n/a
37	chr6:30033850-30033900	LNCaP	prostate:	n/a
38	chr6:30033850-30033900	HRCEpiC	kidney:	n/a
39	chr6:30033850-30033900	PrEC	prostate:	n/a
40	chr6:30033850-30033900	U87	brain:	n/a
41	chr6:30033850-30033900	RPTEC	kidney:	n/a
42	chr6:30033850-30033900	HPAEpiC	pulmonary alveolar:	n/a
43	chr6:30033850-30033900	IMR90	lung:	fetal
44	chr6:30033850-30033900	GM06990	blood:	n/a
45	chr6:30033850-30033900	T-47D	breast:	n/a
46	chr6:30033850-30033900	H1-hESC	embryonic stem cell:	embryo
47	chr6:30033850-30033900	Hela-S3	cervix:	n/a
48	chr6:30033850-30033900	HEK293	kidney:	embryo
49	chr6:30033850-30033900	PANC-1	pancreas:	n/a
50	chr6:30033850-30033900	HEEpiC	esophagus:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30033185..30035212-chr6:30180473..30182741,2	MCF-7	breast:
2	chr6:30032984..30034592-chr6:30523078..30524933,2	K562	blood:
3	chr6:27777374..27779571-chr6:30031951..30033939,2	MCF-7	breast:
4	chr6:30033618..30036318-chr6:30097659..30102068,3	MCF-7	breast:

No data

Variant related genes	Relation type
ZNRD1-AS1	TF binding region
PPP1R11	TF binding region
ZNRD1-AS1	CpG island
PPP1R11	CpG island
ENSG00000234127	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000252228	Chromatin interaction
ENSG00000204576	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10947050	0.93[AFR][1000 genomes]
rs11752303	0.80[AFR][1000 genomes]
rs12200084	0.93[AFR][1000 genomes]
rs33959627	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3910312	0.96[AFR][1000 genomes]
rs4711207	0.96[AFR][1000 genomes]
rs4711209	0.93[AFR][1000 genomes]
rs4713274	0.80[AFR][1000 genomes]
rs4713275	0.80[AFR][1000 genomes]
rs4713281	0.96[AFR][1000 genomes]
rs4947244	0.93[AFR][1000 genomes]
rs4959040	0.93[AFR][1000 genomes]
rs6457127	0.94[AFR][1000 genomes]
rs7767188	0.80[EUR][1000 genomes]
rs9295825	0.82[AFR][1000 genomes]
rs9295829	0.96[AFR][1000 genomes]
rs9295830	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348835	0.93[AFR][1000 genomes]
rs9357092	0.87[AFR][1000 genomes]
rs9366750	0.82[AFR][1000 genomes]
rs9366752	0.91[AFR][1000 genomes]
rs9393986	0.96[AFR][1000 genomes]
rs9393987	0.96[AFR][1000 genomes]
rs9405044	0.96[AFR][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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3807031	HLA-A	cis	lymphoblastoid	seeQTL
rs3807031	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30030000-30034200	Weak transcription	Left Ventricle	heart
2	chr6:30030000-30034200	Weak transcription	Ovary	ovary
3	chr6:30030200-30034000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:30030200-30034000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:30030200-30034000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:30030200-30034000	Weak transcription	Aorta	Aorta
7	chr6:30030200-30034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:30030200-30034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:30030200-30034200	Weak transcription	Lung	lung
10	chr6:30030200-30034400	Weak transcription	Spleen	Spleen
11	chr6:30030800-30034400	Weak transcription	Gastric	stomach
12	chr6:30032800-30034000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:30033200-30034000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:30033200-30034000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:30033400-30034000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:30033400-30034000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:30033400-30034000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:30033400-30034000	Enhancers	Fetal Intestine Large	intestine
19	chr6:30033600-30034000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:30033600-30034000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:30033600-30034000	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:30033600-30034000	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:30033600-30034000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:30033600-30034000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:30033600-30034000	Enhancers	Fetal Muscle Leg	muscle
26	chr6:30033600-30034000	Enhancers	Fetal Stomach	stomach
27	chr6:30033600-30034000	Enhancers	Stomach Mucosa	stomach
28	chr6:30033600-30034000	Flanking Active TSS	Thymus	Thymus
29	chr6:30033600-30034000	Enhancers	HUVEC	blood vessel
30	chr6:30033600-30034200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:30033600-30034200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:30033600-30034200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:30033600-30034200	Enhancers	Brain Substantia Nigra	brain
34	chr6:30033600-30034200	Flanking Active TSS	Fetal Brain Female	brain
35	chr6:30033600-30034200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr6:30033600-30034200	Flanking Active TSS	GM12878-XiMat	blood
37	chr6:30033600-30034400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:30033600-30034400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr6:30033600-30034400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr6:30033600-30034400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:30033600-30034400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr6:30033600-30034400	Flanking Active TSS	Dnd41	blood
43	chr6:30033600-30034600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr6:30033600-30034600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:30033600-30034600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:30033600-30034600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr6:30033600-30035800	Active TSS	A549	lung
48	chr6:30033800-30034000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:30033800-30034000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr6:30033800-30034000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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