Variant report

Variant	rs6681402
Chromosome Location	chr1:85527506-85527507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr1:85527339-85528403	GM12878	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913
2	SP1	chr1:85527500-85528299	HCT-116	colon:	n/a	chr1:85527901-85527922
3	SIN3AK20	chr1:85527456-85528365	PANC-1	pancreas:	n/a	n/a
4	KAP1	chr1:85527437-85528606	HEK293	kidney:	n/a	n/a
5	KAP1	chr1:85527501-85528336	U2OS	brain:	n/a	n/a
6	SP1	chr1:85527454-85528206	HCT-116	colon:	n/a	chr1:85527901-85527922
7	CREB1	chr1:85527355-85528262	GM12878	blood:	n/a	chr1:85527883-85527896
8	POLR2A	chr1:85527261-85527732	SK-N-MC	brain:	n/a	n/a
9	SIN3A	chr1:85527492-85528465	H1-hESC	embryonic stem cell:	n/a	chr1:85527838-85527848
10	CREB1	chr1:85527404-85528200	H1-hESC	embryonic stem cell:	n/a	chr1:85527883-85527896
11	RFX5	chr1:85527345-85528668	SK-N-SH	brain:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
12	RUNX3	chr1:85527411-85528423	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85527490-85527540	Hela-S3	cervix:	n/a
2	chr1:85527490-85527540	NH-A	brain:	n/a
3	chr1:85527490-85527540	SAEC	small airway:	n/a
4	chr1:85527490-85527540	A549	lung:	n/a
5	chr1:85527490-85527540	MCF10A-Er-Src	breast:	n/a
6	chr1:85527490-85527540	HL-60	blood:	n/a
7	chr1:85527490-85527540	Hepatocyte	liver:	n/a
8	chr1:85527490-85527540	HAEpiC	amniotic membrane:	n/a
9	chr1:85527490-85527540	SK-N-SH	brain:	n/a
10	chr1:85527490-85527540	Caco-2	colon:	n/a
11	chr1:85527490-85527540	CMK	blood:	n/a
12	chr1:85527490-85527540	HIPEpiC	eye:	n/a
13	chr1:85527490-85527540	BJ	skin:	n/a
14	chr1:85527490-85527540	MCF-7	breast:	n/a
15	chr1:85527490-85527540	AG09309	skin:	n/a
16	chr1:85527490-85527540	RPTEC	kidney:	n/a
17	chr1:85527490-85527540	HRPEpiC	eye:	n/a
18	chr1:85527490-85527540	HEK293	kidney:	embryo
19	chr1:85527490-85527540	NHBE	bronchial:	n/a
20	chr1:85527490-85527540	Jurkat	blood:	n/a
21	chr1:85527490-85527540	IMR90	lung:	fetal
22	chr1:85527490-85527540	ProgFib	skin:	n/a
23	chr1:85527490-85527540	SKMC	muscle:	n/a
24	chr1:85527490-85527540	GM12878	blood:	n/a
25	chr1:85527490-85527540	H1-hESC	embryonic stem cell:	embryo
26	chr1:85527490-85527540	AG04450	lung:	fetal
27	chr1:85527490-85527540	HCF	heart:	n/a
28	chr1:85527490-85527540	GM06990	blood:	n/a
29	chr1:85527490-85527540	GM12891	blood:	n/a
30	chr1:85527490-85527540	HCT-116	colon:	n/a
31	chr1:85527490-85527540	AG10803	skin:	n/a
32	chr1:85527490-85527540	T-47D	breast:	n/a
33	chr1:85527490-85527540	HRE	kidney:	n/a
34	chr1:85527490-85527540	ECC-1	luminal epithelium:	n/a
35	chr1:85527490-85527540	GM19239	blood:	n/a
36	chr1:85527490-85527540	NHDF-neo	bronchial:	n/a
37	chr1:85527490-85527540	HEEpiC	esophagus:	n/a
38	chr1:85527490-85527540	SK-N-MC	brain:	n/a
39	chr1:85527490-85527540	HMEC	breast:	n/a
40	chr1:85527490-85527540	AoSMC	blood vessel:	n/a
41	chr1:85527490-85527540	SK-N-SH_RA	brain:	n/a
42	chr1:85527490-85527540	HepG2	liver:	n/a
43	chr1:85527490-85527540	HRCEpiC	kidney:	n/a
44	chr1:85527490-85527540	PANC-1	pancreas:	n/a
45	chr1:85527490-85527540	BE2_C	brain:	n/a
46	chr1:85527490-85527540	HUVEC	blood vessel:	n/a
47	chr1:85527490-85527540	HCPEpiC	choroid plexus:	n/a
48	chr1:85527490-85527540	U87	brain:	n/a
49	chr1:85527490-85527540	HPAEpiC	pulmonary alveolar:	n/a
50	chr1:85527490-85527540	AG04449	skin:	fetal

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85520949..85522755-chr1:85525126..85527721,2	K562	blood:

No data

Variant related genes	Relation type
WDR63	TF binding region
WDR63	CpG island

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10782538	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17099213	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs17119333	1.00[CHB][hapmap]
rs17119338	1.00[CHB][hapmap]
rs17120570	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1809249	0.90[EUR][1000 genomes]
rs2165076	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41383647	1.00[CHB][hapmap]
rs41461649	1.00[CHB][hapmap]
rs4243775	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907020	0.81[ASN][1000 genomes]
rs4907127	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4907129	0.81[ASN][1000 genomes]
rs4907130	0.90[CEU][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907131	0.90[CEU][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907132	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6576745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6695223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697585	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7527292	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs7529904	1.00[CHB][hapmap]
rs898035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85527200-85527600	Active TSS	Muscle Satellite Cultured Cells	--
2	chr1:85527200-85527600	Bivalent Enhancer	Fetal Brain Male	brain
3	chr1:85527200-85527600	Active TSS	Right Atrium	heart
4	chr1:85527200-85528000	Active TSS	GM12878-XiMat	blood
5	chr1:85527200-85528200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:85527200-85528400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:85527400-85527600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:85527400-85527600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:85527400-85527600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:85527400-85527600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:85527400-85527600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:85527400-85527600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr1:85527400-85527600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:85527400-85527600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:85527400-85527600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:85527400-85527600	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr1:85527400-85527600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr1:85527400-85527600	Flanking Active TSS	Fetal Brain Female	brain
19	chr1:85527400-85527600	Flanking Active TSS	Fetal Lung	lung
20	chr1:85527400-85527600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr1:85527400-85527600	Active TSS	HSMM	muscle
22	chr1:85527400-85527600	Active TSS	Osteobl	bone
23	chr1:85527400-85527800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:85527400-85527800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:85527400-85527800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr1:85527400-85527800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:85527400-85527800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr1:85527400-85527800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:85527400-85527800	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr1:85527400-85527800	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr1:85527400-85527800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
32	chr1:85527400-85527800	Flanking Active TSS	HMEC	breast
33	chr1:85527400-85527800	Flanking Active TSS	HSMMtube	muscle
34	chr1:85527400-85527800	Active TSS	K562	blood
35	chr1:85527400-85528000	Active TSS	H1 Cell Line	embryonic stem cell
36	chr1:85527400-85528000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:85527400-85528000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr1:85527400-85528000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:85527400-85528000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:85527400-85528000	Active TSS	Brain Hippocampus Middle	brain
41	chr1:85527400-85528000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr1:85527400-85528000	Active TSS	NHEK	skin
43	chr1:85527400-85528200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:85527400-85528200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:85527400-85528200	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:85527400-85528200	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:85527400-85528200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:85527400-85528200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:85527400-85528200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:85527400-85528200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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