Variant report

Variant	rs2743925
Chromosome Location	chr6:29698050-29698051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr6:29697998-29698383	GM12878	blood:	n/a	n/a
2	NFATC1	chr6:29695785-29699667	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:29690658-29699867	GM12891	blood:	n/a	n/a
4	MTA3	chr6:29697513-29698463	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:29697624-29699488	GM19193	blood:	n/a	n/a
6	BCLAF1	chr6:29696998-29698204	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:29697446-29698904	GM12891	blood:	n/a	n/a
8	PML	chr6:29695415-29699000	GM12878	blood:	n/a	n/a
9	NFIC	chr6:29697429-29698138	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:29695163-29699574	GM19099	blood:	n/a	n/a
11	POLR2A	chr6:29694623-29699123	GM12892	blood:	n/a	n/a
12	MTA3	chr6:29695276-29699589	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:29690785-29699707	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:29697492-29698899	GM12891	blood:	n/a	n/a
15	BCLAF1	chr6:29697493-29698069	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:29697456-29698831	GM12878	blood:	n/a	n/a
17	ATF2	chr6:29697444-29698318	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:29690681-29699847	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:29697516-29698069	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:29690708-29699614	GM18505	blood:	n/a	n/a
21	POLR2A	chr6:29690566-29699452	GM12892	blood:	n/a	n/a
22	NFATC1	chr6:29695654-29699504	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:29696196-29699754	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr6:29698035-29698543	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr6:29697460-29698972	GM12892	blood:	n/a	n/a
26	POLR2A	chr6:29695365-29699302	GM18526	blood:	n/a	n/a
27	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:29695198-29698947	GM12891	blood:	n/a	n/a
29	POLR2A	chr6:29695038-29699514	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:29697472-29699003	GM12892	blood:	n/a	n/a
31	STAT5A	chr6:29697427-29699390	GM12878	blood:	n/a	n/a
32	CTCF	chr6:29697796-29698059	K562	blood:	n/a	n/a
33	POLR2A	chr6:29695270-29699448	GM18951	blood:	n/a	n/a
34	POLR2A	chr6:29697488-29698969	GM12891	blood:	n/a	n/a
35	STAT5A	chr6:29697587-29698382	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:
2	chr6:29686730..29689127-chr6:29696614..29698519,2	K562	blood:

No data

Variant related genes	Relation type
RPL23AP1	TF binding region
ENSG00000204642	Chromatin interaction
ENSG00000225864	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2517913	0.86[EUR][1000 genomes]
rs2517933	0.82[AFR][1000 genomes]
rs2517934	0.82[AFR][1000 genomes]
rs2517938	0.84[EUR][1000 genomes]
rs2517941	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2517943	0.86[EUR][1000 genomes]
rs2523385	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2523390	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2523401	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2523407	0.82[AFR][1000 genomes]
rs2735063	0.85[EUR][1000 genomes]
rs2743950	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2844833	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2844845	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs422343	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs730858	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9258126	0.84[EUR][1000 genomes]
rs9258127	0.84[EUR][1000 genomes]
rs9258131	0.83[EUR][1000 genomes]
rs9258255	0.89[AFR][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	nsv462673	chr6:29689590-29700183	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv601230	chr6:29689590-29700183	Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv883531	chr6:29692562-29705402	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2743925	HLA-H	cis	multi-tissue	Pritchard
rs2743925	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2743925	BTN3A1	cis	parietal	SCAN
rs2743925	HLA-A	cis	multi-tissue	Pritchard
rs2743925	HLA-F	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29701800	Weak transcription	HMEC	breast
2	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
6	chr6:29693400-29700000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
8	chr6:29693600-29715600	Weak transcription	NHLF	lung
9	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
12	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:29694000-29711400	Weak transcription	Gastric	stomach
15	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
16	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:29694200-29701800	Weak transcription	NHEK	skin
18	chr6:29694200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:29696000-29702200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:29696000-29705600	Weak transcription	Right Ventricle	heart
21	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:29696000-29715600	Weak transcription	Ovary	ovary
23	chr6:29696200-29699600	Weak transcription	Thymus	Thymus
24	chr6:29696200-29701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:29696200-29701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:29696200-29702200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:29696200-29703800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:29696200-29703800	Weak transcription	Left Ventricle	heart
29	chr6:29696200-29705600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:29696200-29705800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:29696200-29711800	Weak transcription	Adipose Nuclei	Adipose
32	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:29696200-29715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:29696200-29715600	Weak transcription	Liver	Liver
35	chr6:29696400-29699400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:29696400-29699800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:29696400-29700000	Weak transcription	Primary T cells from cord blood	blood
38	chr6:29696400-29701800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:29696400-29701800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:29696400-29702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:29696400-29710800	Weak transcription	Lung	lung
42	chr6:29696400-29711400	Weak transcription	Spleen	Spleen
43	chr6:29696400-29711800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:29696400-29712000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:29696400-29715400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:29696600-29698200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:29696600-29698600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:29696600-29700600	Weak transcription	Primary B cells from cord blood	blood
49	chr6:29696600-29702200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:29696600-29702200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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