Variant report

Variant	rs6682900
Chromosome Location	chr1:246952399-246952400
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:246952160-246952987	NB4	blood:	n/a	n/a
2	POLR2A	chr1:246952110-246952686	NB4	blood:	n/a	n/a
3	BACH1	chr1:246952177-246952496	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr1:246952177-246952705	NB4	blood:	n/a	n/a
5	HMGN3	chr1:246952303-246952614	K562	blood:	n/a	n/a
6	ZBTB7A	chr1:246952335-246952525	K562	blood:	n/a	n/a
7	POLR2A	chr1:246952019-246955465	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:246952362-246952412	PrEC	prostate:	n/a
2	chr1:246952362-246952412	SKMC	muscle:	n/a
3	chr1:246952362-246952412	HL-60	blood:	n/a
4	chr1:246952362-246952412	HUVEC	blood vessel:	n/a
5	chr1:246952362-246952412	Jurkat	blood:	n/a
6	chr1:246952362-246952412	HRCEpiC	kidney:	n/a
7	chr1:246952362-246952412	NH-A	brain:	n/a
8	chr1:246952362-246952412	ovcar-3	ovarian:	n/a
9	chr1:246952362-246952412	NHDF-neo	bronchial:	n/a
10	chr1:246952362-246952412	Caco-2	colon:	n/a
11	chr1:246952362-246952412	SAEC	small airway:	n/a
12	chr1:246952362-246952412	HCF	heart:	n/a
13	chr1:246952362-246952412	AG09319	gingival:	n/a
14	chr1:246952362-246952412	HIPEpiC	eye:	n/a
15	chr1:246952362-246952412	PFSK-1	brain:	n/a
16	chr1:246952362-246952412	HRE	kidney:	n/a
17	chr1:246952362-246952412	AG04449	skin:	fetal
18	chr1:246952362-246952412	HEEpiC	esophagus:	n/a
19	chr1:246952362-246952412	GM12892	blood:	n/a
20	chr1:246952362-246952412	HPAEpiC	pulmonary alveolar:	n/a
21	chr1:246952362-246952412	AG04450	lung:	fetal
22	chr1:246952362-246952412	SK-N-MC	brain:	n/a
23	chr1:246952362-246952412	HCM	heart:	n/a
24	chr1:246952362-246952412	LNCaP	prostate:	n/a
25	chr1:246952362-246952412	A549	lung:	n/a
26	chr1:246952362-246952412	IMR90	lung:	fetal
27	chr1:246952362-246952412	H1-hESC	embryonic stem cell:	embryo
28	chr1:246952362-246952412	BE2_C	brain:	n/a
29	chr1:246952362-246952412	HAEpiC	amniotic membrane:	n/a
30	chr1:246952362-246952412	NHBE	bronchial:	n/a
31	chr1:246952362-246952412	PANC-1	pancreas:	n/a
32	chr1:246952362-246952412	NT2-D1	testis:	n/a
33	chr1:246952362-246952412	Hepatocyte	liver:	n/a
34	chr1:246952362-246952412	SK-N-SH_RA	brain:	n/a
35	chr1:246952362-246952412	GM19239	blood:	n/a
36	chr1:246952362-246952412	GM12878	blood:	n/a
37	chr1:246952362-246952412	T-47D	breast:	n/a
38	chr1:246952362-246952412	K562	blood:	n/a
39	chr1:246952362-246952412	NB4	blood:	n/a
40	chr1:246952362-246952412	HNPCEpiC	eye:	n/a
41	chr1:246952362-246952412	MCF10A-Er-Src	breast:	n/a
42	chr1:246952362-246952412	BJ	skin:	n/a
43	chr1:246952362-246952412	GM06990	blood:	n/a
44	chr1:246952362-246952412	MCF-7	breast:	n/a
45	chr1:246952362-246952412	HepG2	liver:	n/a
46	chr1:246952362-246952412	HEK293	kidney:	embryo
47	chr1:246952362-246952412	HCPEpiC	choroid plexus:	n/a
48	chr1:246952362-246952412	HMEC	breast:	n/a
49	chr1:246952362-246952412	CMK	blood:	n/a
50	chr1:246952362-246952412	Hela-S3	cervix:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCCPDH-1	chr1:246952396-246953000	ENSG00000227953.2

No data

Variant related genes	Relation type
ENSG00000227953	TF binding region
ENSG00000227953	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1127098	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1127149	0.88[ASN][1000 genomes]
rs12121187	0.81[ASN][1000 genomes]
rs12128579	0.81[ASN][1000 genomes]
rs12129386	0.81[ASN][1000 genomes]
rs12402095	0.98[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12403128	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12409066	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12410595	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3087781	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35021082	0.81[AMR][1000 genomes]
rs3795469	0.90[ASN][1000 genomes]
rs4078128	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs41310575	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4926440	0.88[ASN][1000 genomes]
rs4926442	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4926443	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4926444	0.92[ASN][1000 genomes]
rs4926447	0.85[AMR][1000 genomes]
rs4926449	0.88[ASN][1000 genomes]
rs4926450	0.90[ASN][1000 genomes]
rs4926456	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61684731	0.81[ASN][1000 genomes]
rs61852479	0.80[ASN][1000 genomes]
rs61852481	0.81[ASN][1000 genomes]
rs61852482	0.81[ASN][1000 genomes]
rs6699332	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7365254	0.85[AMR][1000 genomes]
rs7366187	0.81[ASN][1000 genomes]
rs74152239	0.86[ASN][1000 genomes]
rs7513496	0.82[ASN][1000 genomes]
rs7526237	0.81[ASN][1000 genomes]
rs7528002	0.86[ASN][1000 genomes]
rs7550482	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv1841827	chr1:246944502-246954313	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:246941200-246952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:246945800-246956400	Weak transcription	A549	lung
6	chr1:246946200-246952400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:246946200-246956800	Weak transcription	Left Ventricle	heart
8	chr1:246949000-246952400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:246949000-246957600	Weak transcription	NHDF-Ad	bronchial
10	chr1:246949200-246952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:246949200-246952800	Weak transcription	Spleen	Spleen
12	chr1:246949200-246953000	Weak transcription	Gastric	stomach
13	chr1:246949400-246956800	Weak transcription	Hela-S3	cervix
14	chr1:246949400-246957600	Weak transcription	NHLF	lung
15	chr1:246951000-246952600	Enhancers	Liver	Liver
16	chr1:246951200-246954800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:246951400-246952800	Enhancers	Placenta	Placenta
18	chr1:246951600-246952400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:246951600-246952400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:246951600-246952600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:246951600-246953400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:246951800-246953000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:246952000-246952400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:246952000-246952400	Active TSS	Rectal Smooth Muscle	rectum
25	chr1:246952000-246952600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:246952000-246952600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:246952000-246952600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:246952000-246952600	Active TSS	Brain Anterior Caudate	brain
29	chr1:246952000-246952600	Enhancers	Fetal Lung	lung
30	chr1:246952000-246952600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr1:246952000-246952600	Active TSS	Fetal Stomach	stomach
32	chr1:246952000-246952600	Active TSS	Osteobl	bone
33	chr1:246952000-246952800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr1:246952000-246952800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:246952000-246952800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:246952000-246952800	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr1:246952000-246952800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr1:246952000-246952800	Enhancers	GM12878-XiMat	blood
39	chr1:246952000-246953000	Enhancers	Fetal Heart	heart
40	chr1:246952000-246953200	Flanking Active TSS	Fetal Thymus	thymus
41	chr1:246952000-246953400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr1:246952000-246953400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:246952000-246953400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:246952200-246952400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr1:246952200-246952400	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:246952200-246952400	Enhancers	Primary B cells from cord blood	blood
47	chr1:246952200-246952400	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr1:246952200-246952400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr1:246952200-246952400	Active TSS	Primary hematopoietic stem cells	blood
50	chr1:246952200-246952400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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