Variant report

Variant	rs6681619
Chromosome Location	chr1:85527701-85527702
allele	A/C
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	NFYA	chr1:85527628-85528133	GM12878	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527918 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913
2	PBX3	chr1:85527687-85528169	A549	lung:	n/a	chr1:85527968-85527977
3	PBX3	chr1:85527659-85528275	SK-N-SH	brain:	n/a	chr1:85527968-85527977
4	PBX3	chr1:85527576-85528298	SK-N-SH	brain:	n/a	chr1:85527968-85527977
5	RUNX3	chr1:85527671-85528275	GM12878	blood:	n/a	n/a
6	SP2	chr1:85527681-85528090	K562	blood:	n/a	n/a
7	SP1	chr1:85527665-85528161	GM12878	blood:	n/a	chr1:85527901-85527922
8	MAZ	chr1:85527597-85528039	GM12878	blood:	n/a	n/a
9	SP2	chr1:85527550-85528175	H1-hESC	embryonic stem cell:	n/a	n/a
10	NFYB	chr1:85527339-85528403	GM12878	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913
11	SP1	chr1:85527500-85528299	HCT-116	colon:	n/a	chr1:85527901-85527922
12	SP1	chr1:85527530-85528241	A549	lung:	n/a	chr1:85527901-85527922
13	CHD2	chr1:85527590-85528136	GM12878	blood:	n/a	n/a
14	WRNIP1	chr1:85527573-85528308	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr1:85527696-85528357	PANC-1	pancreas:	n/a	n/a
16	SIN3AK20	chr1:85527456-85528365	PANC-1	pancreas:	n/a	n/a
17	KAP1	chr1:85527437-85528606	HEK293	kidney:	n/a	n/a
18	POLR2A	chr1:85527650-85528165	HCT-116	colon:	n/a	n/a
19	SP1	chr1:85527656-85528234	A549	lung:	n/a	chr1:85527901-85527922
20	CREB1	chr1:85527523-85528198	GM12878	blood:	n/a	chr1:85527883-85527896
21	CREB1	chr1:85527622-85528139	HepG2	liver:	n/a	chr1:85527883-85527896
22	SIN3AK20	chr1:85527551-85528226	H1-hESC	embryonic stem cell:	n/a	n/a
23	CREB1	chr1:85527558-85528208	H1-hESC	embryonic stem cell:	n/a	chr1:85527883-85527896
24	RFX5	chr1:85527701-85528180	GM12878	blood:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
25	SP1	chr1:85527609-85528239	H1-hESC	embryonic stem cell:	n/a	chr1:85527901-85527922
26	CREB1	chr1:85527637-85528181	ECC-1	luminal epithelium:	n/a	chr1:85527883-85527896
27	NFYB	chr1:85527639-85528166	K562	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913
28	ATF1	chr1:85527690-85528130	K562	blood:	n/a	n/a
29	KAP1	chr1:85527501-85528336	U2OS	brain:	n/a	n/a
30	SP2	chr1:85527653-85528133	H1-hESC	embryonic stem cell:	n/a	n/a
31	ATF2	chr1:85527606-85528207	GM12878	blood:	n/a	chr1:85527884-85527895
32	SP1	chr1:85527454-85528206	HCT-116	colon:	n/a	chr1:85527901-85527922
33	CREB1	chr1:85527518-85528102	A549	lung:	n/a	chr1:85527883-85527896
34	CREB1	chr1:85527355-85528262	GM12878	blood:	n/a	chr1:85527883-85527896
35	POLR2A	chr1:85527261-85527732	SK-N-MC	brain:	n/a	n/a
36	SIN3A	chr1:85527492-85528465	H1-hESC	embryonic stem cell:	n/a	chr1:85527838-85527848
37	SP1	chr1:85527678-85528393	GM12878	blood:	n/a	chr1:85527901-85527922
38	CREB1	chr1:85527404-85528200	H1-hESC	embryonic stem cell:	n/a	chr1:85527883-85527896
39	RFX5	chr1:85527345-85528668	SK-N-SH	brain:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
40	RUNX3	chr1:85527411-85528423	GM12878	blood:	n/a	n/a
41	CREB1	chr1:85527566-85528218	K562	blood:	n/a	chr1:85527883-85527896
42	CREB1	chr1:85527689-85528084	ECC-1	luminal epithelium:	n/a	chr1:85527883-85527896

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

Variant related genes	Relation type
WDR63	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10782538	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873684	0.88[YRI][hapmap]
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];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs17119333	1.00[CHB][hapmap]
rs17119338	1.00[CHB][hapmap]
rs17120570	0.86[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs1809249	0.90[EUR][1000 genomes]
rs2012369	0.86[YRI][hapmap]
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]
rs4907126	0.82[YRI][hapmap]
rs4907127	0.89[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];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4907131	0.90[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][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[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681402	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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697585	0.84[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7527292	0.90[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6681619	MCOLN2	cis	parietal	SCAN
rs6681619	WDR63	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85527200-85528000	Active TSS	GM12878-XiMat	blood
2	chr1:85527200-85528200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:85527200-85528400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:85527400-85527800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:85527400-85527800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:85527400-85527800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr1:85527400-85527800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:85527400-85527800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr1:85527400-85527800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:85527400-85527800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:85527400-85527800	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr1:85527400-85527800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
13	chr1:85527400-85527800	Flanking Active TSS	HMEC	breast
14	chr1:85527400-85527800	Flanking Active TSS	HSMMtube	muscle
15	chr1:85527400-85527800	Active TSS	K562	blood
16	chr1:85527400-85528000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr1:85527400-85528000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:85527400-85528000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:85527400-85528000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:85527400-85528000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:85527400-85528000	Active TSS	Brain Hippocampus Middle	brain
22	chr1:85527400-85528000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr1:85527400-85528000	Active TSS	NHEK	skin
24	chr1:85527400-85528200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:85527400-85528200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:85527400-85528200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:85527400-85528200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:85527400-85528200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:85527400-85528200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:85527400-85528200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:85527400-85528200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:85527400-85528200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:85527400-85528200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
34	chr1:85527400-85528200	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr1:85527400-85528200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr1:85527400-85528200	Active TSS	Brain Cingulate Gyrus	brain
37	chr1:85527400-85528200	Active TSS	Colonic Mucosa	Colon
38	chr1:85527400-85528200	Active TSS	Duodenum Mucosa	Duodenum
39	chr1:85527400-85528200	Active TSS	Fetal Heart	heart
40	chr1:85527400-85528200	Active TSS	Fetal Intestine Large	intestine
41	chr1:85527400-85528200	Active TSS	Fetal Intestine Small	intestine
42	chr1:85527400-85528200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr1:85527400-85528200	Flanking Active TSS	Fetal Thymus	thymus
44	chr1:85527400-85528200	Active TSS	Rectal Smooth Muscle	rectum
45	chr1:85527400-85528200	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:85527400-85528200	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:85527400-85528200	Active TSS	Thymus	Thymus
48	chr1:85527400-85528200	Active TSS	NHDF-Ad	bronchial
49	chr1:85527400-85528400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr1:85527400-85528400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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