Variant report

Variant	rs2523405
Chromosome Location	chr6:29695305-29695306
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	POLR2A	chr6:29690658-29699867	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:29695149-29697426	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:29695188-29697002	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:29695131-29697353	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:29695163-29699574	GM19099	blood:	n/a	n/a
6	POLR2A	chr6:29694623-29699123	GM12892	blood:	n/a	n/a
7	MTA3	chr6:29695276-29699589	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:29695304-29697234	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:29690785-29699707	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:29690681-29699847	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:29690708-29699614	GM18505	blood:	n/a	n/a
12	POLR2A	chr6:29690566-29699452	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:29690657-29697457	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:29690594-29697494	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:29695198-29698947	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:29695079-29697466	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:29695038-29699514	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:29695270-29699448	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29691971..29693668-chr6:29693958..29696725,2	K562	blood:
2	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:

Variant related genes	Relation type
HCG4P11	TF binding region
RPL23AP1	TF binding region
ENSG00000225864	Chromatin interaction
ENSG00000204642	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1362125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362126	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610741	0.82[ASN][1000 genomes]
rs2076176	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107184	0.89[ASN][1000 genomes]
rs2394159	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394160	0.89[ASN][1000 genomes]
rs2394162	0.82[ASN][1000 genomes]
rs2517939	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2523387	0.88[ASN][1000 genomes]
rs2523388	0.89[ASN][1000 genomes]
rs2523389	0.88[ASN][1000 genomes]
rs2523393	0.89[ASN][1000 genomes]
rs2523395	0.90[ASN][1000 genomes]
rs2523396	0.90[ASN][1000 genomes]
rs2523397	0.90[ASN][1000 genomes]
rs2523402	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2523404	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735051	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2735052	0.90[ASN][1000 genomes]
rs2735057	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735062	0.84[EUR][1000 genomes]
rs2743917	0.89[ASN][1000 genomes]
rs2743918	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2743919	0.89[ASN][1000 genomes]
rs2743922	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743949	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2743951	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844830	0.87[ASN][1000 genomes]
rs2844831	0.89[ASN][1000 genomes]
rs2844832	0.89[ASN][1000 genomes]
rs2844846	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3998799	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4248137	0.83[EUR][1000 genomes]
rs4248138	0.83[EUR][1000 genomes]
rs4988549	0.84[ASN][1000 genomes]
rs6457009	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv970101	chr6:29692268-29695615	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	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
12	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:44)

SNP	Gene	Cis/trans	Tissue	Source
rs2523405	HCG4P5	cis	Thyroid	GTEx
rs2523405	ZFP57	cis	Whole Blood	GTEx
rs2523405	HLA-A	cis	Artery Tibial	GTEx
rs2523405	HCG4P5	cis	Artery Tibial	GTEx
rs2523405	NDUFS1	trans	multi-tissue	Pritchard
rs2523405	HCG4P5	cis	Skin Sun Exposed Lower leg	GTEx
rs2523405	HLA-J	cis	Skin Sun Exposed Lower leg	GTEx
rs2523405	HLA.A29.1	cis	multi-tissue	Pritchard
rs2523405	HCG4P11	cis	Whole Blood	GTEx
rs2523405	HCG4P5	cis	Whole Blood	GTEx
rs2523405	HCG4	cis	multi-tissue	Pritchard
rs2523405	HLA-J	cis	Artery Tibial	GTEx
rs2523405	ZFP57	cis	Esophagus Mucosa	GTEx
rs2523405	HCG4P5	cis	Muscle Skeletal	GTEx
rs2523405	HLA-J	cis	Muscle Skeletal	GTEx
rs2523405	HLA-J	cis	Esophagus Mucosa	GTEx
rs2523405	HLA-J	cis	Thyroid	GTEx
rs2523405	HLA-J	cis	Adipose Subcutaneous	GTEx
rs2523405	HCG4P5	cis	Esophagus Muscularis	GTEx
rs2523405	HLA-J	cis	Esophagus Muscularis	GTEx
rs2523405	HLA-J	cis	Whole Blood	GTEx
rs2523405	HLA-A	cis	Nerve Tibial	GTEx
rs2523405	HLA-J	cis	lung	GTEx
rs2523405	HLA-H	cis	lymphoblastoid	seeQTL
rs2523405	HCG4P5	cis	lung	GTEx
rs2523405	HLA-A	cis	brain	seeQTL
rs2523405	HLA-H	cis	multi-tissue	Pritchard
rs2523405	HLA-G	cis	multi-tissue	Pritchard
rs2523405	KIT	trans	multi-tissue	Pritchard
rs2523405	HCG4P5	cis	Nerve Tibial	GTEx
rs2523405	HCG4P5	cis	Stomach	GTEx
rs2523405	HLA-A	cis	multi-tissue	Pritchard
rs2523405	HCG4P5	cis	Heart Left Ventricle	GTEx
rs2523405	TFG	trans	multi-tissue	Pritchard
rs2523405	ZFP57	cis	Skin Sun Exposed Lower leg	GTEx
rs2523405	TPD52L2	trans	multi-tissue	Pritchard
rs2523405	HCG4P5	cis	Adipose Subcutaneous	GTEx
rs2523405	HLA-F	cis	Whole Blood	GTEx
rs2523405	HLA-A	cis	lymphoblastoid	seeQTL
rs2523405	HCG4P5	cis	Artery Aorta	GTEx
rs2523405	HLA-F	cis	multi-tissue	Pritchard
rs2523405	HLA-J	cis	Nerve Tibial	GTEx
rs2523405	ZFP57	cis	Artery Tibial	GTEx
rs2523405	ZSCAN23	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29691200-29695400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
2	chr6:29692200-29701800	Weak transcription	HMEC	breast
3	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:29692400-29695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:29692600-29696200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:29692600-29696400	Genic enhancers	Spleen	Spleen
8	chr6:29692600-29697400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:29692800-29696000	Strong transcription	Primary hematopoietic stem cells	blood
10	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:29693200-29696200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
13	chr6:29693400-29696000	Strong transcription	Right Ventricle	heart
14	chr6:29693400-29697000	Weak transcription	Fetal Thymus	thymus
15	chr6:29693400-29700000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
17	chr6:29693600-29696200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:29693600-29696800	Weak transcription	Fetal Intestine Large	intestine
19	chr6:29693600-29697600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:29693600-29715600	Weak transcription	NHLF	lung
21	chr6:29693800-29696000	Strong transcription	Ovary	ovary
22	chr6:29693800-29696400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
26	chr6:29694000-29696000	Strong transcription	Left Ventricle	heart
27	chr6:29694000-29696200	Strong transcription	Adipose Nuclei	Adipose
28	chr6:29694000-29696200	Strong transcription	Liver	Liver
29	chr6:29694000-29696200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:29694000-29696400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:29694000-29696400	Strong transcription	Lung	lung
32	chr6:29694000-29696400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:29694000-29696400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:29694000-29696600	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr6:29694000-29696600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:29694000-29696600	Strong transcription	Brain Anterior Caudate	brain
37	chr6:29694000-29696600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:29694000-29696800	Strong transcription	Colonic Mucosa	Colon
39	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:29694000-29711400	Weak transcription	Gastric	stomach
42	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
43	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:29694200-29695800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:29694200-29695800	Strong transcription	Stomach Mucosa	stomach
46	chr6:29694200-29696000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:29694200-29696200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:29694200-29696200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:29694200-29696200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr6:29694200-29696200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood

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