Variant report

Variant	rs2799079
Chromosome Location	chr6:28235176-28235177
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr6:28234699-28235328	GM12878	blood:	n/a	chr6:28235002-28235011
2	ELF1	chr6:28234701-28235213	GM12878	blood:	n/a	n/a
3	SP1	chr6:28234715-28235230	A549	lung:	n/a	chr6:28235096-28235108 chr6:28235098-28235107 chr6:28235097-28235107 chr6:28235093-28235107 chr6:28235096-28235108 chr6:28235097-28235107 chr6:28235098-28235107 chr6:28235097-28235106
4	POLR2A	chr6:28234535-28235399	HUVEC	blood vessel:	n/a	n/a
5	YY1	chr6:28234438-28235488	SK-N-SH_RA	brain:	n/a	chr6:28234608-28234618 chr6:28235097-28235106
6	FOXA1	chr6:28234750-28235287	HepG2	liver:	n/a	n/a
7	POU2F2	chr6:28234627-28235186	GM12878	blood:	n/a	n/a
8	MYBL2	chr6:28234635-28235532	HepG2	liver:	n/a	n/a
9	MTA3	chr6:28234609-28235520	GM12878	blood:	n/a	n/a
10	YY1	chr6:28234420-28235250	K562	blood:	n/a	chr6:28234608-28234618 chr6:28235097-28235106
11	POLR2A	chr6:28234779-28235464	HepG2	liver:	n/a	n/a
12	RUNX3	chr6:28234667-28235504	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:28234705-28235249	HUVEC	blood vessel:	n/a	n/a
14	REST	chr6:28234304-28236278	H1-neurons	neurons:	n/a	chr6:28235001-28235011 chr6:28234996-28235009
15	FOXA1	chr6:28234738-28235388	HepG2	liver:	n/a	n/a
16	UBTF	chr6:28234738-28235410	K562	blood:	n/a	n/a
17	POLR2A	chr6:28234625-28235183	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:28234613-28235230	K562	blood:	n/a	n/a
19	POLR2A	chr6:28234566-28235279	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr6:28234574-28235664	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr6:28234590-28235299	U87	brain:	n/a	n/a
22	GABPA	chr6:28234709-28235264	K562	blood:	n/a	chr6:28235097-28235106
23	POLR2A	chr6:28234590-28235305	U87	brain:	n/a	n/a
24	SP2	chr6:28234554-28235277	H1-hESC	embryonic stem cell:	n/a	chr6:28235017-28235032
25	POLR2A	chr6:28234635-28235227	Gliobla	brain:	n/a	n/a
26	CBX3	chr6:28234619-28235489	K562	blood:	n/a	n/a
27	POLR2A	chr6:28234631-28235219	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:28234592-28235571	ProgFib	skin:	n/a	n/a
29	POLR2A	chr6:28234649-28235208	Hela-S3	cervix:	n/a	n/a
30	NR2F2	chr6:28234511-28235549	K562	blood:	n/a	n/a
31	RCOR1	chr6:28234689-28235297	Hela-S3	cervix:	n/a	n/a
32	TAF1	chr6:28234690-28235541	H1-neurons	neurons:	n/a	n/a
33	POLR2A	chr6:28234688-28235257	MCF-7	breast:	n/a	n/a
34	KAP1	chr6:28234487-28235195	U2OS	brain:	n/a	n/a
35	ELF1	chr6:28234708-28235262	HepG2	liver:	n/a	n/a
36	SP2	chr6:28234604-28235465	K562	blood:	n/a	chr6:28235017-28235032
37	FOXP2	chr6:28234959-28235249	SK-N-MC	brain:	n/a	n/a
38	SMC3	chr6:28234744-28235319	Hela-S3	cervix:	n/a	n/a
39	EGR1	chr6:28234696-28235294	K562	blood:	n/a	chr6:28235091-28235106 chr6:28235092-28235105
40	HEY1	chr6:28234650-28235265	K562	blood:	n/a	n/a
41	EBF1	chr6:28234774-28235321	GM12878	blood:	n/a	chr6:28235124-28235135
42	ZNF263	chr6:28234728-28235327	HEK293-T-REx	kidney:	n/a	n/a
43	MAX	chr6:28234891-28235420	HepG2	liver:	n/a	chr6:28235095-28235105
44	YY1	chr6:28234486-28235229	GM12892	blood:	n/a	chr6:28234608-28234618 chr6:28235097-28235106
45	POLR2A	chr6:28234559-28235283	GM12892	blood:	n/a	n/a
46	CCNT2	chr6:28234845-28235217	K562	blood:	n/a	chr6:28235097-28235106
47	POLR2A	chr6:28234552-28235447	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr6:28234638-28235407	GM19099	blood:	n/a	n/a
49	POLR2A	chr6:28234669-28235182	U87	brain:	n/a	n/a
50	GABPA	chr6:28234537-28235492	MCF-7	breast:	n/a	chr6:28235097-28235106

No.	Distal block	Cell Line	Cell type
1	chr6:28232839..28237434-chr6:28303380..28305726,5	MCF-7	breast:
2	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
3	chr6:28232995..28235984-chr6:28248211..28251032,3	MCF-7	breast:
4	chr6:28218740..28220554-chr6:28234465..28236739,2	MCF-7	breast:
5	chr6:28230426..28232674-chr6:28234865..28236670,2	K562	blood:
6	chr6:28234639..28236512-chr6:28285629..28288301,2	K562	blood:
7	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
8	chr2:28766464..28767325-chr6:28234791..28235488,2	MCF-7	breast:
9	chr6:28048448..28050071-chr6:28234359..28236283,2	K562	blood:
10	chr6:28233569..28236323-chr6:28583574..28585743,2	K562	blood:
11	chr15:48826718..48827238-chr6:28234952..28235665,2	HCT-116	colon:
12	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
13	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
14	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:
15	chr6:28191934..28194357-chr6:28233804..28235938,2	MCF-7	breast:
16	chr6:28234828..28238066-chr6:28314810..28319280,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197062	TF binding region
ENSG00000272009	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000270326	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10456362	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1076639	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs11755032	0.81[CHB][hapmap];0.89[CHD][hapmap];0.89[ASN][1000 genomes]
rs11965538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000	0.91[YRI][hapmap]
rs13200462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1321505	0.93[CEU][hapmap]
rs1339899	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs1419183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778507	0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[ASN][1000 genomes]
rs1778508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1936365	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213239	0.81[CHB][hapmap]
rs213241	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs213243	0.81[CHB][hapmap]
rs213244	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs2743554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[ASN][1000 genomes]
rs2743555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757188	0.93[CEU][hapmap]
rs4713139	0.93[CEU][hapmap]
rs4713140	0.93[CEU][hapmap]
rs68141011	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6901575	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap]
rs6905391	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920512	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs735765	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7740487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853676	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853678	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853679	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853681	0.86[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853682	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853685	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853687	0.80[ASN][1000 genomes]
rs853688	0.89[ASN][1000 genomes]
rs853694	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295765	0.81[CHB][hapmap]
rs9366717	0.93[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[EUR][1000 genomes]
rs9368561	0.80[EUR][1000 genomes]
rs9380064	0.93[CEU][hapmap]
rs9380069	0.93[CEU][hapmap]
rs9393908	0.81[EUR][1000 genomes]
rs9461446	0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[ASN][1000 genomes]
rs9461448	0.81[CHB][hapmap];0.89[CHD][hapmap];0.89[ASN][1000 genomes]
rs9461449	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs9468287	0.93[CEU][hapmap]
rs9468318	0.81[CEU][hapmap]
rs9468321	0.81[CHB][hapmap];0.91[ASN][1000 genomes]
rs9468322	0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[ASN][1000 genomes]
rs9468342	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs9468345	0.81[CHB][hapmap]
rs9986596	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2799079	HLA-A	cis	multi-tissue	Pritchard
rs2799079	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2799079	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2799079	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2799079	RP5-874C20.3	cis	Thyroid	GTEx
rs2799079	ENSG00000197062	cis	multi-tissue	Pritchard
rs2799079	AL022393.7	cis	Muscle Skeletal	GTEx
rs2799079	ZNF307	cis	multi-tissue	Pritchard
rs2799079	BTN3A2	cis	multi-tissue	Pritchard
rs2799079	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs2799079	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28233800-28235800	Active TSS	Brain Hippocampus Middle	brain
2	chr6:28233800-28236400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28234000-28235600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:28234000-28235600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:28234000-28235800	Active TSS	Fetal Kidney	kidney
6	chr6:28234000-28235800	Active TSS	Stomach Smooth Muscle	stomach
7	chr6:28234000-28236000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:28234000-28236000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:28234200-28235200	Active TSS	Adipose Nuclei	Adipose
10	chr6:28234200-28235200	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:28234200-28235400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:28234200-28235400	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr6:28234200-28235400	Active TSS	HMEC	breast
14	chr6:28234200-28235400	Active TSS	K562	blood
15	chr6:28234200-28235600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:28234200-28235600	Active TSS	Fetal Brain Male	brain
17	chr6:28234200-28235600	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr6:28234200-28235600	Active TSS	Osteobl	bone
19	chr6:28234200-28235800	Active TSS	NHDF-Ad	bronchial
20	chr6:28234200-28236000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:28234200-28236000	Active TSS	Fetal Stomach	stomach
22	chr6:28234200-28236000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:28234200-28236000	Active TSS	A549	lung
24	chr6:28234200-28236200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr6:28234200-28236400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:28234200-28236400	Active TSS	NHLF	lung
27	chr6:28234400-28235200	Active TSS	Primary monocytes fromperipheralblood	blood
28	chr6:28234400-28235200	Active TSS	Primary B cells from peripheral blood	blood
29	chr6:28234400-28235200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr6:28234400-28235200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:28234400-28235200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:28234400-28235200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:28234400-28235200	Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:28234400-28235200	Active TSS	Brain Angular Gyrus	brain
35	chr6:28234400-28235200	Active TSS	Placenta	Placenta
36	chr6:28234400-28235200	Active TSS	Fetal Thymus	thymus
37	chr6:28234400-28235200	Active TSS	Thymus	Thymus
38	chr6:28234400-28235200	Active TSS	NH-A	brain
39	chr6:28234400-28235400	Active TSS	Primary T cells fromperipheralblood	blood
40	chr6:28234400-28235400	Active TSS	Colon Smooth Muscle	Colon
41	chr6:28234400-28235400	Active TSS	Duodenum Mucosa	Duodenum
42	chr6:28234400-28235400	Active TSS	GM12878-XiMat	blood
43	chr6:28234400-28235600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:28234400-28235600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:28234400-28235600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:28234400-28235600	Active TSS	Aorta	Aorta
47	chr6:28234400-28235600	Active TSS	Brain Anterior Caudate	brain
48	chr6:28234400-28235600	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:28234400-28235600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:28234400-28235600	Active TSS	Fetal Muscle Trunk	muscle

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