Variant report

Variant	rs2844845
Chromosome Location	chr6:29712759-29712760
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29712707..29714647-chr6:29717488..29720857,3	K562	blood:
2	chr6:29710008..29711886-chr6:29712365..29714063,2	K562	blood:
3	chr6:29712194..29714049-chr6:29781280..29783856,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFP57-7	chr6:29712727-29713011	NONHSAT108548

Variant related genes	Relation type
ENSG00000272236	Chromatin interaction
ENSG00000199290	Chromatin interaction
ENSG00000235821	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1611283	0.81[ASN][1000 genomes]
rs1611285	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508050	0.89[ASN][1000 genomes]
rs2517913	0.81[EUR][1000 genomes]
rs2517933	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517934	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517938	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517941	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517943	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523385	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523390	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523401	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2523407	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735063	0.80[EUR][1000 genomes]
rs2743925	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2743950	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422343	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730858	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258255	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258256	0.87[EUR][1000 genomes]
rs9258278	1.00[ASN][1000 genomes]
rs9258285	0.84[ASN][1000 genomes]
rs9258294	1.00[ASN][1000 genomes]
rs9258305	1.00[ASN][1000 genomes]
rs9258373	0.96[ASN][1000 genomes]
rs9258384	1.00[ASN][1000 genomes]
rs9258393	1.00[ASN][1000 genomes]
rs9258434	0.89[ASN][1000 genomes]
rs9258441	0.93[ASN][1000 genomes]
rs9258451	0.82[ASN][1000 genomes]
rs9258508	0.89[ASN][1000 genomes]
rs9258525	0.89[ASN][1000 genomes]
rs9258605	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2844845	BTN3A1	cis	parietal	SCAN
rs2844845	HIST1H2BE	cis	parietal	SCAN
rs2844845	HLA-H	cis	multi-tissue	Pritchard
rs2844845	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

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	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
4	chr6:29693600-29715600	Weak transcription	NHLF	lung
5	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
7	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:29696000-29715600	Weak transcription	Ovary	ovary
10	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:29696200-29715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:29696200-29715600	Weak transcription	Liver	Liver
13	chr6:29696400-29715400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:29696600-29715600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:29696800-29714600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:29696800-29715800	Weak transcription	Colonic Mucosa	Colon
17	chr6:29700000-29715200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:29702400-29715400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:29702600-29715400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:29702800-29712800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:29702800-29713800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:29702800-29715400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:29702800-29715600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:29706000-29715400	Weak transcription	Right Atrium	heart
25	chr6:29706000-29715800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:29706800-29715800	Weak transcription	NHDF-Ad	bronchial
27	chr6:29707400-29713000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:29707600-29715400	Weak transcription	NHEK	skin
29	chr6:29708800-29713200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:29709800-29714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:29709800-29715400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:29710800-29713200	Strong transcription	Lung	lung
33	chr6:29711200-29712800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:29711200-29713000	Strong transcription	Right Ventricle	heart
35	chr6:29711200-29713600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:29711200-29715200	Weak transcription	HMEC	breast
37	chr6:29711400-29713000	Strong transcription	Gastric	stomach
38	chr6:29711400-29713400	Strong transcription	Pancreas	Pancrea
39	chr6:29711400-29713600	Strong transcription	Spleen	Spleen
40	chr6:29711400-29713800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:29711600-29713000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr6:29711800-29713400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:29712000-29713200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr6:29712000-29714000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:29712200-29712800	Strong transcription	Aorta	Aorta
46	chr6:29712400-29713400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:29712400-29713800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:29712400-29715400	Weak transcription	Left Ventricle	heart
49	chr6:29712400-29715600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:29712400-29715600	Weak transcription	Monocytes-CD14+_RO01746	blood

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