Variant report

Variant	rs885946
Chromosome Location	chr6:29696657-29696658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr6:29695785-29699667	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:29690658-29699867	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:29695149-29697426	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:29695427-29697285	GM15510	blood:	n/a	n/a
5	PML	chr6:29695415-29699000	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:29695188-29697002	GM12891	blood:	n/a	n/a
7	POLR2A	chr6:29695131-29697353	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:29695163-29699574	GM19099	blood:	n/a	n/a
9	POLR2A	chr6:29694623-29699123	GM12892	blood:	n/a	n/a
10	MTA3	chr6:29695276-29699589	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:29695304-29697234	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:29690785-29699707	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	NFATC1	chr6:29695654-29699504	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:29696196-29699754	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:29690657-29697457	GM12892	blood:	n/a	n/a
21	POLR2A	chr6:29695365-29699302	GM18526	blood:	n/a	n/a
22	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:29690594-29697494	GM12878	blood:	n/a	n/a
24	STAT5A	chr6:29696137-29696873	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:29695198-29698947	GM12891	blood:	n/a	n/a
26	POLR2A	chr6:29695079-29697466	GM12892	blood:	n/a	n/a
27	POLR2A	chr6:29695038-29699514	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:29696518-29696933	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr6:29696444-29696708	GM12878	blood:	n/a	n/a
30	BCLAF1	chr6:29695785-29696868	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:29695270-29699448	GM18951	blood:	n/a	n/a
32	ZNF143	chr6:29696362-29696795	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:29695318-29697307	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29696650-29696700	NHBE	bronchial:	n/a
2	chr6:29696647-29696697	HRPEpiC	eye:	n/a
3	chr6:29696650-29696700	NHDF-neo	bronchial:	n/a
4	chr6:29696647-29696697	HEEpiC	esophagus:	n/a
5	chr6:29696647-29696697	AG10803	skin:	n/a
6	chr6:29696647-29696697	SAEC	small airway:	n/a
7	chr6:29696650-29696700	SKMC	muscle:	n/a
8	chr6:29696647-29696697	SKMC	muscle:	n/a
9	chr6:29696650-29696700	Hepatocyte	liver:	n/a
10	chr6:29696647-29696697	PFSK-1	brain:	n/a
11	chr6:29696650-29696700	ovcar-3	ovarian:	n/a
12	chr6:29696650-29696700	HCF	heart:	n/a
13	chr6:29696650-29696700	HRPEpiC	eye:	n/a
14	chr6:29696650-29696700	U87	brain:	n/a
15	chr6:29696650-29696700	SK-N-MC	brain:	n/a
16	chr6:29696647-29696697	SK-N-MC	brain:	n/a
17	chr6:29696647-29696697	U87	brain:	n/a
18	chr6:29696650-29696700	HMEC	breast:	n/a
19	chr6:29696647-29696697	HCPEpiC	choroid plexus:	n/a
20	chr6:29696650-29696700	AG04450	lung:	fetal
21	chr6:29696650-29696700	HUVEC	blood vessel:	n/a
22	chr6:29696647-29696697	IMR90	lung:	fetal
23	chr6:29696647-29696697	Caco-2	colon:	n/a
24	chr6:29696650-29696700	AG04449	skin:	fetal
25	chr6:29696647-29696697	NT2-D1	testis:	n/a
26	chr6:29696647-29696697	AoSMC	blood vessel:	n/a
27	chr6:29696650-29696700	HNPCEpiC	eye:	n/a
28	chr6:29696650-29696700	NT2-D1	testis:	n/a
29	chr6:29696650-29696700	GM12892	blood:	n/a
30	chr6:29696650-29696700	AG09309	skin:	n/a
31	chr6:29696650-29696700	HRE	kidney:	n/a
32	chr6:29696650-29696700	GM19239	blood:	n/a
33	chr6:29696647-29696697	NHDF-neo	bronchial:	n/a
34	chr6:29696650-29696700	PFSK-1	brain:	n/a
35	chr6:29696650-29696700	NH-A	brain:	n/a
36	chr6:29696650-29696700	HCT-116	colon:	n/a
37	chr6:29696650-29696700	PrEC	prostate:	n/a
38	chr6:29696650-29696700	GM06990	blood:	n/a
39	chr6:29696650-29696700	HepG2	liver:	n/a
40	chr6:29696650-29696700	GM12878	blood:	n/a
41	chr6:29696647-29696697	RPTEC	kidney:	n/a
42	chr6:29696647-29696697	AG04449	skin:	fetal
43	chr6:29696647-29696697	Hela-S3	cervix:	n/a
44	chr6:29696647-29696697	H1-hESC	embryonic stem cell:	embryo
45	chr6:29696647-29696697	GM06990	blood:	n/a
46	chr6:29696647-29696697	HAEpiC	amniotic membrane:	n/a
47	chr6:29696650-29696700	H1-hESC	embryonic stem cell:	embryo
48	chr6:29696647-29696697	BE2_C	brain:	n/a
49	chr6:29696647-29696697	Hepatocyte	liver:	n/a
50	chr6:29696650-29696700	SK-N-SH	brain:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:29691971..29693668-chr6:29693958..29696725,2	K562	blood:
2	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:
3	chr6:29686730..29689127-chr6:29696614..29698519,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MOG-2	chr6:29695734-29697128	NONHSAT108542

No data

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

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1419696	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1610601	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1610602	0.85[ASN][1000 genomes]
rs1610608	0.83[ASN][1000 genomes]
rs1610612	0.85[ASN][1000 genomes]
rs1610617	0.82[ASN][1000 genomes]
rs1610621	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1610625	0.80[ASN][1000 genomes]
rs1610629	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1610633	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1610729	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1610735	0.81[ASN][1000 genomes]
rs1622223	0.80[ASN][1000 genomes]
rs1628578	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1632957	0.85[ASN][1000 genomes]
rs1632960	0.80[ASN][1000 genomes]
rs1633063	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1633088	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1633096	0.85[ASN][1000 genomes]
rs1633098	0.85[ASN][1000 genomes]
rs1633099	0.85[ASN][1000 genomes]
rs1633106	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1633107	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1736915	0.85[ASN][1000 genomes]
rs1737077	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2517911	0.81[ASN][1000 genomes]
rs3129036	0.80[EUR][1000 genomes]
rs885942	0.85[ASN][1000 genomes]
rs885943	0.85[ASN][1000 genomes]
rs885944	0.85[ASN][1000 genomes]
rs885945	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs929158	0.85[ASN][1000 genomes]
rs929159	0.85[ASN][1000 genomes]
rs929160	0.84[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	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs885946	ZFP57	cis	Adipose Subcutaneous	GTEx
rs885946	ZFP57	cis	Skin Sun Exposed Lower leg	GTEx
rs885946	ZFP57	cis	Artery Tibial	GTEx
rs885946	ZFP57	cis	Thyroid	GTEx
rs885946	ZFP57	cis	Whole Blood	GTEx
rs885946	ZFP57	cis	Esophagus Mucosa	GTEx
rs885946	HLA-F-AS1	cis	Whole Blood	GTEx
rs885946	ZFP57	cis	Heart Left Ventricle	GTEx
rs885946	IFITM4P	cis	Thyroid	GTEx
rs885946	ZFP57	cis	Artery Aorta	GTEx
rs885946	ZFP57	cis	lung	GTEx
rs885946	ZFP57	cis	Nerve Tibial	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	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:29692600-29697400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
7	chr6:29693400-29697000	Weak transcription	Fetal Thymus	thymus
8	chr6:29693400-29700000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
10	chr6:29693600-29696800	Weak transcription	Fetal Intestine Large	intestine
11	chr6:29693600-29697600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:29693600-29715600	Weak transcription	NHLF	lung
13	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
16	chr6:29694000-29696800	Strong transcription	Colonic Mucosa	Colon
17	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:29694000-29711400	Weak transcription	Gastric	stomach
20	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
21	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:29694200-29696800	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr6:29694200-29696800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:29694200-29697000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:29694200-29701800	Weak transcription	NHEK	skin
26	chr6:29694200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:29694600-29696800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr6:29694600-29697800	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:29694800-29696800	Strong transcription	GM12878-XiMat	blood
30	chr6:29695000-29696800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:29695400-29696800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr6:29695800-29697600	Weak transcription	Fetal Intestine Small	intestine
33	chr6:29695800-29697600	Weak transcription	Stomach Mucosa	stomach
34	chr6:29696000-29702200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:29696000-29705600	Weak transcription	Right Ventricle	heart
36	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:29696000-29715600	Weak transcription	Ovary	ovary
38	chr6:29696200-29697600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:29696200-29697600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:29696200-29697600	Weak transcription	Placenta	Placenta
41	chr6:29696200-29699600	Weak transcription	Thymus	Thymus
42	chr6:29696200-29701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:29696200-29701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:29696200-29702200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:29696200-29703800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:29696200-29703800	Weak transcription	Left Ventricle	heart
47	chr6:29696200-29705600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:29696200-29705800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:29696200-29711800	Weak transcription	Adipose Nuclei	Adipose
50	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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