Variant report

Variant	rs2073723
Chromosome Location	chr6:31130078-31130079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:31129030-31131105	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr6:31129877-31130427	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF7	chr6:31130065-31130929	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:31129133-31130873	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF2	chr6:31129758-31130460	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:31128767-31131569	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:31129049-31131566	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr6:31130019-31130607	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:31130042-31131132	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:31128357-31133697	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:7278546..7279417-chr6:31129910..31130580,2	MCF-7	breast:
2	chr6:31129675..31131961-chr6:31164663..31167424,2	K562	blood:
3	chr6:31130035..31132882-chr6:31132970..31134557,3	MCF-7	breast:
4	chr6:31126958..31132315-chr6:31135299..31140140,6	K562	blood:
5	chr6:31129596..31132185-chr6:31285768..31288675,2	MCF-7	breast:
6	chr6:31129733..31135466-chr6:31137398..31140077,6	K562	blood:

No data

Variant related genes	Relation type
CCHCR1	TF binding region
ENSG00000272501	Chromatin interaction
ENSG00000204531	Chromatin interaction
ENSG00000206344	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1061118	0.84[ASN][1000 genomes]
rs1065461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs130078	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2022084	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073719	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2073721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073722	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2106074	0.82[ASN][1000 genomes]
rs2240059	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240065	0.82[AMR][1000 genomes]
rs2394882	0.84[ASN][1000 genomes]
rs3094192	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094194	0.87[ASN][1000 genomes]
rs3094226	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094227	0.86[AMR][1000 genomes]
rs3130450	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130451	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130452	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130456	0.80[ASN][1000 genomes]
rs3130498	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130499	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130500	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130501	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130502	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130503	0.82[AMR][1000 genomes]
rs3130504	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130575	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130928	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130929	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130931	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3130932	0.82[ASN][1000 genomes]
rs3130934	0.84[ASN][1000 genomes]
rs3132522	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132523	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132524	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132535	0.90[ASN][1000 genomes]
rs743401	0.80[ASN][1000 genomes]
rs9263787	0.80[ASN][1000 genomes]
rs9263804	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
13	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
14	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2073723	HLA-DQB1	cis	multi-tissue	Pritchard
rs2073723	HLA-DRB5	cis	multi-tissue	Pritchard
rs2073723	HCG27	cis	multi-tissue	Pritchard
rs2073723	HLA-DRB1	cis	multi-tissue	Pritchard
rs2073723	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31127200-31131800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:31127200-31140600	Weak transcription	Left Ventricle	heart
3	chr6:31127200-31146800	Weak transcription	Small Intestine	intestine
4	chr6:31127600-31131800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:31127600-31132600	Weak transcription	Pancreas	Pancrea
6	chr6:31127600-31133000	Weak transcription	Fetal Intestine Large	intestine
7	chr6:31127600-31136600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:31127600-31137000	Weak transcription	Stomach Mucosa	stomach
9	chr6:31127600-31143000	Weak transcription	Right Ventricle	heart
10	chr6:31127600-31147800	Weak transcription	Primary B cells from cord blood	blood
11	chr6:31127600-31148000	Weak transcription	Right Atrium	heart
12	chr6:31127800-31130200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:31127800-31130400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:31127800-31130400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:31127800-31130800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:31127800-31131400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:31127800-31131400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:31127800-31131400	Weak transcription	Fetal Kidney	kidney
19	chr6:31127800-31131600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:31127800-31132400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:31127800-31132600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:31127800-31132600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:31127800-31132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:31127800-31132800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:31127800-31133000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:31127800-31136400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:31127800-31136400	Weak transcription	Primary T cells from cord blood	blood
28	chr6:31127800-31142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:31127800-31142800	Weak transcription	HSMM	muscle
30	chr6:31127800-31146200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:31127800-31147800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:31127800-31147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:31127800-31153200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:31128000-31130200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:31128000-31130400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:31128000-31130400	Weak transcription	A549	lung
37	chr6:31128000-31130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:31128000-31131600	Weak transcription	Fetal Heart	heart
39	chr6:31128000-31131800	Weak transcription	NH-A	brain
40	chr6:31128000-31132800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:31128000-31135600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:31128000-31136800	Weak transcription	K562	blood
43	chr6:31128000-31137400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:31128000-31140400	Weak transcription	Brain Germinal Matrix	brain
45	chr6:31128000-31143200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:31128200-31130600	Weak transcription	NHEK	skin
47	chr6:31128200-31131200	Genic enhancers	Dnd41	blood
48	chr6:31128200-31133200	Weak transcription	HUVEC	blood vessel
49	chr6:31128200-31135800	Weak transcription	Fetal Brain Female	brain
50	chr6:31128200-31143600	Weak transcription	NHDF-Ad	bronchial

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