Variant report

Variant	rs2735060
Chromosome Location	chr6:29695466-29695467
allele	A/T
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	chr6:29695427-29697285	GM15510	blood:	n/a	n/a
4	PML	chr6:29695415-29699000	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:29695188-29697002	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:29695131-29697353	GM12891	blood:	n/a	n/a
7	POLR2A	chr6:29695163-29699574	GM19099	blood:	n/a	n/a
8	POLR2A	chr6:29694623-29699123	GM12892	blood:	n/a	n/a
9	MTA3	chr6:29695276-29699589	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:29695304-29697234	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:29690785-29699707	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr6:29695462-29695691	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:29695342-29697252	GM19193	blood:	n/a	n/a
14	POLR2A	chr6:29690681-29699847	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:29690708-29699614	GM18505	blood:	n/a	n/a
16	STAT5A	chr6:29695345-29696882	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:29690566-29699452	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:29690657-29697457	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:29695326-29695721	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:29695365-29699302	GM18526	blood:	n/a	n/a
21	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
22	POLR2A	chr6:29690594-29697494	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:29695198-29698947	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:29695079-29697466	GM12892	blood:	n/a	n/a
25	POLR2A	chr6:29695038-29699514	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:29695318-29696429	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:29695270-29699448	GM18951	blood:	n/a	n/a
28	POLR2A	chr6:29695318-29697307	GM12878	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
ENSG00000204642	Chromatin interaction
ENSG00000225864	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 32 )

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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523405	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	1.00[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:32)

SNP	Gene	Cis/trans	Tissue	Source
rs2735060	HLA-A	cis	Nerve Tibial	GTEx
rs2735060	HCG4P5	cis	Stomach	GTEx
rs2735060	HCG4P5	cis	lung	GTEx
rs2735060	HLA-A	cis	Artery Tibial	GTEx
rs2735060	HLA-J	cis	Whole Blood	GTEx
rs2735060	HLA-J	cis	Adipose Subcutaneous	GTEx
rs2735060	ZFP57	cis	Skin Sun Exposed Lower leg	GTEx
rs2735060	ZFP57	cis	Whole Blood	GTEx
rs2735060	HCG4P5	cis	Heart Left Ventricle	GTEx
rs2735060	ZFP57	cis	Esophagus Mucosa	GTEx
rs2735060	HCG4P5	cis	Thyroid	GTEx
rs2735060	HCG4P5	cis	Muscle Skeletal	GTEx
rs2735060	HLA.A29.1	cis	multi-tissue	Pritchard
rs2735060	HLA-F	cis	Whole Blood	GTEx
rs2735060	HCG4P5	cis	Esophagus Muscularis	GTEx
rs2735060	HCG4P11	cis	Whole Blood	GTEx
rs2735060	HCG4P5	cis	Nerve Tibial	GTEx
rs2735060	HCG4P5	cis	Artery Tibial	GTEx
rs2735060	HCG4P5	cis	Artery Aorta	GTEx
rs2735060	HLA-J	cis	Esophagus Muscularis	GTEx
rs2735060	HCG4P5	cis	Adipose Subcutaneous	GTEx
rs2735060	HLA-J	cis	Thyroid	GTEx
rs2735060	HLA-J	cis	lung	GTEx
rs2735060	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2735060	HLA-J	cis	Muscle Skeletal	GTEx
rs2735060	HLA-J	cis	Esophagus Mucosa	GTEx
rs2735060	ZFP57	cis	Artery Tibial	GTEx
rs2735060	HCG4P5	cis	Whole Blood	GTEx
rs2735060	HLA-J	cis	Nerve Tibial	GTEx
rs2735060	HLA-J	cis	Skin Sun Exposed Lower leg	GTEx
rs2735060	HLA-J	cis	Artery Tibial	GTEx
rs2735060	HCG4P5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:72 , 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	chr6:29692400-29695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:29692600-29696200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:29692600-29696400	Genic enhancers	Spleen	Spleen
7	chr6:29692600-29697400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:29692800-29696000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:29693200-29696200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
12	chr6:29693400-29696000	Strong transcription	Right Ventricle	heart
13	chr6:29693400-29697000	Weak transcription	Fetal Thymus	thymus
14	chr6:29693400-29700000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
16	chr6:29693600-29696200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:29693600-29696800	Weak transcription	Fetal Intestine Large	intestine
18	chr6:29693600-29697600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:29693600-29715600	Weak transcription	NHLF	lung
20	chr6:29693800-29696000	Strong transcription	Ovary	ovary
21	chr6:29693800-29696400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
25	chr6:29694000-29696000	Strong transcription	Left Ventricle	heart
26	chr6:29694000-29696200	Strong transcription	Adipose Nuclei	Adipose
27	chr6:29694000-29696200	Strong transcription	Liver	Liver
28	chr6:29694000-29696200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:29694000-29696400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr6:29694000-29696400	Strong transcription	Lung	lung
31	chr6:29694000-29696400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:29694000-29696400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr6:29694000-29696600	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr6:29694000-29696600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:29694000-29696600	Strong transcription	Brain Anterior Caudate	brain
36	chr6:29694000-29696600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:29694000-29696800	Strong transcription	Colonic Mucosa	Colon
38	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:29694000-29711400	Weak transcription	Gastric	stomach
41	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
42	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:29694200-29695800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:29694200-29695800	Strong transcription	Stomach Mucosa	stomach
45	chr6:29694200-29696000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:29694200-29696200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:29694200-29696200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:29694200-29696200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr6:29694200-29696200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr6:29694200-29696200	Strong transcription	Rectal Mucosa Donor 31	rectum

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