Variant report

Variant	rs2801951
Chromosome Location	chr10:42970831-42970832
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:42970576-42971231	HCT-116	colon:	n/a	n/a
2	MAX	chr10:42970550-42971438	HCT-116	colon:	n/a	n/a
3	MAX	chr10:42970603-42971501	K562	blood:	n/a	chr10:42971430-42971440
4	CTCF	chr10:42970723-42970836	SK-N-SH_RA	brain:	n/a	n/a
5	MAX	chr10:42970507-42971608	SK-N-SH	brain:	n/a	chr10:42971430-42971440
6	CTCF	chr10:42970780-42970930	AG09309	skin:	n/a	n/a
7	POLR2A	chr10:42970474-42971292	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr10:42970700-42970850	SK-N-SH_RA	brain:	n/a	n/a
9	POLR2A	chr10:42970776-42971710	Gliobla	brain:	n/a	n/a
10	MAX	chr10:42970496-42971535	HCT-116	colon:	n/a	chr10:42971430-42971440
11	USF1	chr10:42970798-42971345	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr10:42970591-42971215	SK-N-SH	brain:	n/a	n/a
13	TAF1	chr10:42970797-42971267	PFSK-1	brain:	n/a	n/a
14	REST	chr10:42970560-42971197	SK-N-SH	brain:	n/a	n/a
15	MXI1	chr10:42969491-42973054	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr10:42970697-42971356	U87	brain:	n/a	n/a
17	USF1	chr10:42970796-42971263	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr10:42970700-42970850	AG09309	skin:	n/a	n/a
19	MAX	chr10:42970582-42971606	SK-N-SH	brain:	n/a	chr10:42971430-42971440
20	SIN3AK20	chr10:42970509-42971381	HCT-116	colon:	n/a	n/a
21	NFYA	chr10:42970819-42970946	K562	blood:	n/a	chr10:42970879-42970897
22	SIN3AK20	chr10:42970488-42971353	SK-N-SH	brain:	n/a	n/a
23	YY1	chr10:42970571-42971197	SK-N-SH_RA	brain:	n/a	n/a
24	TAF1	chr10:42970813-42971153	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr10:42970578-42971247	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr10:42970720-42970870	SK-N-SH_RA	brain:	n/a	n/a
27	NFYB	chr10:42970688-42971036	K562	blood:	n/a	n/a
28	SP1	chr10:42970438-42971368	HCT-116	colon:	n/a	chr10:42970805-42970814
29	YY1	chr10:42970631-42971145	SK-N-SH_RA	brain:	n/a	n/a
30	POLR2A	chr10:42970622-42971564	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr10:42970697-42971261	U87	brain:	n/a	n/a
32	POLR2A	chr10:42970561-42971491	PFSK-1	brain:	n/a	n/a
33	TAF1	chr10:42970561-42971212	SK-N-SH	brain:	n/a	n/a
34	USF1	chr10:42970819-42971208	SK-N-SH_RA	brain:	n/a	n/a
35	POLR2A	chr10:42970580-42971250	HCT-116	colon:	n/a	n/a
36	POLR2A	chr10:42970725-42971472	PANC-1	pancreas:	n/a	n/a
37	CTCF	chr10:42970740-42970890	BE2_C	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:42970785-42970835	HL-60	blood:	n/a
2	chr10:42970785-42970835	IMR90	lung:	fetal
3	chr10:42970785-42970835	K562	blood:	n/a
4	chr10:42970785-42970835	PrEC	prostate:	n/a
5	chr10:42970785-42970835	ProgFib	skin:	n/a
6	chr10:42970785-42970835	HMEC	breast:	n/a
7	chr10:42970785-42970835	ovcar-3	ovarian:	n/a
8	chr10:42970785-42970835	CMK	blood:	n/a
9	chr10:42970785-42970835	BE2_C	brain:	n/a
10	chr10:42970785-42970835	MCF-7	breast:	n/a
11	chr10:42970785-42970835	NH-A	brain:	n/a
12	chr10:42970785-42970835	SK-N-MC	brain:	n/a
13	chr10:42970785-42970835	AG04449	skin:	fetal
14	chr10:42970785-42970835	BJ	skin:	n/a
15	chr10:42970785-42970835	HRE	kidney:	n/a
16	chr10:42970785-42970835	HCT-116	colon:	n/a
17	chr10:42970785-42970835	HIPEpiC	eye:	n/a
18	chr10:42970785-42970835	Hela-S3	cervix:	n/a
19	chr10:42970785-42970835	SKMC	muscle:	n/a
20	chr10:42970785-42970835	GM12891	blood:	n/a
21	chr10:42970785-42970835	SK-N-SH	brain:	n/a
22	chr10:42970785-42970835	NHBE	bronchial:	n/a
23	chr10:42970785-42970835	AG10803	skin:	n/a
24	chr10:42970785-42970835	H1-hESC	embryonic stem cell:	embryo
25	chr10:42970785-42970835	HEEpiC	esophagus:	n/a
26	chr10:42970785-42970835	SAEC	small airway:	n/a
27	chr10:42970785-42970835	HepG2	liver:	n/a
28	chr10:42970785-42970835	PFSK-1	brain:	n/a
29	chr10:42970785-42970835	GM12878	blood:	n/a
30	chr10:42970785-42970835	Caco-2	colon:	n/a
31	chr10:42970785-42970835	NHDF-neo	bronchial:	n/a
32	chr10:42970785-42970835	GM06990	blood:	n/a
33	chr10:42970785-42970835	HCM	heart:	n/a
34	chr10:42970785-42970835	U87	brain:	n/a
35	chr10:42970785-42970835	HPAEpiC	pulmonary alveolar:	n/a
36	chr10:42970785-42970835	HRCEpiC	kidney:	n/a
37	chr10:42970785-42970835	ECC-1	luminal epithelium:	n/a
38	chr10:42970785-42970835	AoSMC	blood vessel:	n/a
39	chr10:42970785-42970835	MCF10A-Er-Src	breast:	n/a
40	chr10:42970785-42970835	HUVEC	blood vessel:	n/a
41	chr10:42970785-42970835	PANC-1	pancreas:	n/a
42	chr10:42970785-42970835	RPTEC	kidney:	n/a
43	chr10:42970785-42970835	GM19239	blood:	n/a
44	chr10:42970785-42970835	HNPCEpiC	eye:	n/a
45	chr10:42970785-42970835	AG09309	skin:	n/a
46	chr10:42970785-42970835	A549	lung:	n/a
47	chr10:42970785-42970835	NT2-D1	testis:	n/a
48	chr10:42970785-42970835	AG04450	lung:	fetal
49	chr10:42970785-42970835	HRPEpiC	eye:	n/a
50	chr10:42970785-42970835	HCPEpiC	choroid plexus:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:42969989..42972327-chr10:43278200..43280239,2	K562	blood:

No data

Variant related genes	Relation type
LINC00839	TF binding region
CCNYL2	TF binding region
LINC00839	CpG island
CCNYL2	CpG island
ENSG00000165733	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1255366	0.88[ASN][1000 genomes]
rs1255367	0.88[ASN][1000 genomes]
rs1255372	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255400	0.82[ASN][1000 genomes]
rs1255407	0.88[ASN][1000 genomes]
rs1255412	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158376	1.00[YRI][hapmap]
rs1760687	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210232	0.84[ASN][1000 genomes]
rs210233	0.81[ASN][1000 genomes]
rs210235	0.81[ASN][1000 genomes]
rs210253	0.81[ASN][1000 genomes]
rs210258	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs210261	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs210262	0.81[ASN][1000 genomes]
rs2982229	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550669	chr10:42725663-42982645	ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv550670	chr10:42725663-43089965	Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv895054	chr10:42761931-43068841	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv466877	chr10:42794125-43066414	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv550683	chr10:42794125-43066414	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv471665	chr10:42852460-43006666	Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1051346	chr10:42864101-43006803	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv895071	chr10:42864138-43066414	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv895073	chr10:42884169-43066505	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
18	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
19	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
21	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
22	nsv947882	chr10:42970371-42973594	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2801951	LINC00839	cis	Artery Aorta	GTEx
rs2801951	LOC84856	cis	parietal	SCAN
rs2801951	LINC00839	cis	Artery Tibial	GTEx
rs2801951	CCNYL2	cis	Artery Aorta	GTEx
rs2801951	LINC00839	cis	Skin Sun Exposed Lower leg	GTEx
rs2801951	LINC00839	cis	Esophagus Muscularis	GTEx
rs2801951	LOC84856	cis	thalamus	BrainEAC
rs2801951	LINC00839	cis	Esophagus Mucosa	GTEx
rs2801951	LINC00839	cis	Thyroid	GTEx
rs2801951	LINC00839	cis	Nerve Tibial	GTEx
rs2801951	LINC00839	cis	lung	GTEx
rs2801951	LOC84856	cis	brain	BrainEAC

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:42970600-42971400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr10:42970600-42971400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
3	chr10:42970600-42971800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:42970600-42972000	Active TSS	Brain Cingulate Gyrus	brain
5	chr10:42970600-42972600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:42970800-42971000	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
7	chr10:42970800-42971000	Weak transcription	Aorta	Aorta
8	chr10:42970800-42971000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr10:42970800-42971000	Active TSS	Stomach Smooth Muscle	stomach
10	chr10:42970800-42971200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:42970800-42971200	Flanking Active TSS	HMEC	breast
12	chr10:42970800-42971400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:42970800-42971800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:42970800-42972000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:42970800-42972000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
16	chr10:42970800-42972000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:42970800-42972000	Active TSS	Brain Angular Gyrus	brain
18	chr10:42970800-42972000	Active TSS	Brain Anterior Caudate	brain
19	chr10:42970800-42972000	ZNF genes & repeats	Fetal Stomach	stomach
20	chr10:42970800-42972200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:42970800-42972200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:42970800-42972200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:42970800-42972200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr10:42970800-42972200	ZNF genes & repeats	Fetal Brain Female	brain
25	chr10:42970800-42972600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:42970800-42972600	Active TSS	Pancreatic Islets	Pancreatic Islet

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