Variant report

Variant	rs2743951
Chromosome Location	chr6:29709234-29709235
allele	A/G
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	POLR2A	chr6:29709193-29709262	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:29708276-29711285	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29692092..29694262-chr6:29708323..29710900,2	K562	blood:
2	chr6:29708611..29711552-chr6:29714400..29717446,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLA-F-2	chr6:29709099-29709632	NONHSAT108546

Variant related genes	Relation type
HLA-F-AS1	TF binding region
ENSG00000227758	Chromatin interaction
ENSG00000273340	Chromatin interaction
ENSG00000214922	Chromatin interaction
ENSG00000204642	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1362125	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1362126	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1610741	0.84[ASN][1000 genomes]
rs1736905	0.84[ASN][1000 genomes]
rs2076176	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2107184	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394159	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394160	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394162	0.83[ASN][1000 genomes]
rs2394164	0.80[ASN][1000 genomes]
rs2517939	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2523387	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523388	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523389	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523393	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523395	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523396	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523397	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523402	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523404	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2523405	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2735051	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2735052	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735057	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2735059	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2735060	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2743917	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2743918	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743919	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2743922	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2743949	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2844830	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844831	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844832	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844846	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3998799	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713242	0.80[ASN][1000 genomes]
rs4988549	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883533	chr6:29704237-29715997	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2743951	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2743951	HIST1H2BM	cis	cerebellum	SCAN
rs2743951	HLA-A	cis	lymphoblastoid	GTEx
rs2743951	HLA-H	cis	lymphoblastoid	seeQTL
rs2743951	HLA-A	cis	lymphoblastoid	seeQTL
rs2743951	HLA.A29.1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
5	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
6	chr6:29693600-29715600	Weak transcription	NHLF	lung
7	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
9	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:29694000-29711400	Weak transcription	Gastric	stomach
11	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
12	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:29696000-29715600	Weak transcription	Ovary	ovary
15	chr6:29696200-29711800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:29696200-29715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:29696200-29715600	Weak transcription	Liver	Liver
19	chr6:29696400-29710800	Weak transcription	Lung	lung
20	chr6:29696400-29711400	Weak transcription	Spleen	Spleen
21	chr6:29696400-29711800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:29696400-29712000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:29696400-29715400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:29696600-29715600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:29696800-29714600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr6:29696800-29715800	Weak transcription	Colonic Mucosa	Colon
27	chr6:29699200-29712400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:29700000-29715200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:29700600-29711600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:29702000-29711200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:29702000-29711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:29702400-29709800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:29702400-29715400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:29702600-29715400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:29702800-29712000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr6:29702800-29712800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:29702800-29713800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:29702800-29715400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:29702800-29715600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:29706000-29712000	Weak transcription	Left Ventricle	heart
41	chr6:29706000-29715400	Weak transcription	Right Atrium	heart
42	chr6:29706000-29715800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:29706200-29711200	Weak transcription	Right Ventricle	heart
44	chr6:29706800-29715800	Weak transcription	NHDF-Ad	bronchial
45	chr6:29707400-29713000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:29707600-29715400	Weak transcription	NHEK	skin
47	chr6:29708400-29711200	Strong transcription	HMEC	breast
48	chr6:29708600-29710000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:29708600-29712600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:29708800-29713200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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