Variant report

Variant	rs6661009
Chromosome Location	chr1:153940739-153940740
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	TAF1	chr1:153939493-153941042	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:153939399-153940861	PFSK-1	brain:	n/a	n/a
3	USF1	chr1:153939401-153940777	HCT-116	colon:	n/a	n/a
4	TBL1XR1	chr1:153939295-153940755	K562	blood:	n/a	n/a
5	POLR2A	chr1:153939520-153941282	K562	blood:	n/a	n/a
6	POLR2A	chr1:153939527-153940748	K562	blood:	n/a	n/a
7	MAX	chr1:153939390-153940758	HepG2	liver:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
8	MAX	chr1:153939304-153941038	HCT-116	colon:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
9	JUN	chr1:153938999-153941490	K562	blood:	n/a	chr1:153940887-153940896 chr1:153940888-153940897
10	SIN3AK20	chr1:153939018-153941202	MCF-7	breast:	n/a	n/a
11	YY1	chr1:153939512-153940762	SK-N-SH_RA	brain:	n/a	chr1:153940669-153940678
12	MYC	chr1:153939235-153941336	K562	blood:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
13	NR2F2	chr1:153939484-153940780	K562	blood:	n/a	n/a
14	YY1	chr1:153939541-153940899	H1-hESC	embryonic stem cell:	n/a	chr1:153940889-153940898 chr1:153940669-153940678
15	MYC	chr1:153939115-153941357	K562	blood:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
16	POLR2A	chr1:153939519-153940818	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr1:153940129-153940833	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:153940620-153940770	BJ	skin:	n/a	n/a
19	SP1	chr1:153939319-153940932	HCT-116	colon:	n/a	chr1:153940670-153940679 chr1:153940888-153940900 chr1:153940670-153940679 chr1:153940889-153940898 chr1:153940669-153940678 chr1:153940885-153940899 chr1:153940665-153940679 chr1:153940668-153940680 chr1:153940890-153940899 chr1:153940668-153940680 chr1:153940888-153940900 chr1:153940669-153940679 chr1:153940669-153940679 chr1:153940890-153940899
20	TAF1	chr1:153939491-153940910	MCF-7	breast:	n/a	n/a
21	TAF7	chr1:153939509-153940768	H1-hESC	embryonic stem cell:	n/a	n/a
22	STAT3	chr1:153939660-153940784	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr1:153939130-153940820	PBDE	blood:	n/a	n/a
24	POLR2A	chr1:153938327-153941368	H1-hESC	embryonic stem cell:	n/a	n/a
25	MXI1	chr1:153938969-153941793	SK-N-SH	brain:	n/a	chr1:153939837-153939846
26	TBP	chr1:153939566-153940826	H1-hESC	embryonic stem cell:	n/a	n/a
27	PML	chr1:153939170-153941054	GM12878	blood:	n/a	n/a
28	E2F6	chr1:153939524-153940794	K562	blood:	n/a	chr1:153940669-153940678
29	EP300	chr1:153940441-153940976	T-47D	breast:	n/a	n/a
30	CTCF	chr1:153939477-153941309	SK-N-SH	brain:	n/a	chr1:153939750-153939763
31	YY1	chr1:153939498-153940761	SK-N-SH	brain:	n/a	chr1:153940669-153940678
32	SIN3AK20	chr1:153939275-153940921	HCT-116	colon:	n/a	n/a
33	REST	chr1:153939330-153941029	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr1:153939516-153940775	GM19193	blood:	n/a	n/a
35	POLR2A	chr1:153939430-153940794	ProgFib	skin:	n/a	n/a
36	CHD2	chr1:153939552-153940806	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr1:153939529-153940756	GM18951	blood:	n/a	n/a
38	MTA3	chr1:153938335-153940835	GM12878	blood:	n/a	n/a
39	MAX	chr1:153939484-153941389	MCF-7	breast:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
40	HCFC1	chr1:153938960-153941500	Hela-S3	cervix:	n/a	n/a
41	PML	chr1:153939459-153940841	MCF-7	breast:	n/a	n/a
42	MYC	chr1:153939522-153940802	Hela-S3	cervix:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
43	POLR2A	chr1:153939139-153940850	HCT-116	colon:	n/a	n/a
44	MYC	chr1:153939098-153940742	A549	lung:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
45	POLR2A	chr1:153939541-153941315	K562	blood:	n/a	n/a
46	POLR2A	chr1:153939111-153940961	HCT-116	colon:	n/a	n/a
47	POLR2A	chr1:153939050-153940975	Hela-S3	cervix:	n/a	n/a
48	SP4	chr1:153939715-153940776	H1-hESC	embryonic stem cell:	n/a	chr1:153940666-153940682
49	TAF1	chr1:153939557-153940765	H1-hESC	embryonic stem cell:	n/a	n/a
50	FOXA1	chr1:153940568-153940870	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153936330..153941464-chr1:154191669..154195552,8	MCF-7	breast:
2	chr1:153940232..153940968-chr16:70834699..70835404,2	Hela-S3	cervix:
3	chr1:153738608..153741004-chr1:153939988..153941617,2	MCF-7	breast:
4	chr1:153938901..153941053-chr16:89004507..89006484,2	MCF-7	breast:
5	chr1:153939660..153941891-chr17:61903372..61905744,2	MCF-7	breast:
6	chr1:153641625..153644878-chr1:153937648..153941391,3	K562	blood:
7	chr1:153581488..153584174-chr1:153940194..153943077,2	MCF-7	breast:
8	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
9	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
10	chr1:153603827..153606641-chr1:153939224..153941084,2	MCF-7	breast:
11	chr1:153938202..153942686-chr1:154154566..154158952,5	MCF-7	breast:
12	chr1:153940285..153941977-chr1:154154150..154156390,2	MCF-7	breast:
13	chr1:153939104..153942755-chr1:154191760..154194945,4	MCF-7	breast:
14	chr1:153747624..153749302-chr1:153940489..153942860,2	MCF-7	breast:
15	chr1:153940375..153941059-chr11:62558792..62559444,2	HCT-116	colon:
16	chr1:153939194..153941936-chr6:27857839..27860043,2	MCF-7	breast:

Variant related genes	Relation type
SLC39A1	TF binding region
CREB3L4	TF binding region
ENSG00000197153	Chromatin interaction
ENSG00000087191	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000108592	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000205018	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000261226	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000103043	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10127484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908525	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908526	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908578	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs11264573	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264621	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800001	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12142639	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12142733	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap]
rs17364880	1.00[JPT][hapmap]
rs2252508	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2790686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs2841108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap]
rs3001365	1.00[CHB][hapmap]
rs35711150	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791186	0.84[EUR][1000 genomes]
rs4276953	0.80[EUR][1000 genomes]
rs4845360	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4845586	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671362	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7414227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521047	0.81[MEX][hapmap]
rs7522030	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7537213	0.81[MEX][hapmap]
rs7549032	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6661009	CTAG2	trans	parietal	SCAN
rs6661009	FLG	cis	parietal	SCAN
rs6661009	SLC27A3	cis	cerebellum	SCAN
rs6661009	GATAD2B	cis	cerebellum	SCAN
rs6661009	SLC25A44	cis	parietal	SCAN
rs6661009	PSMD4	cis	parietal	SCAN
rs6661009	S100A8	cis	parietal	SCAN
rs6661009	HAX1	cis	cerebellum	SCAN
rs6661009	GBA	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153938400-153941000	Active TSS	A549	lung
2	chr1:153938400-153941400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:153938600-153941200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:153938800-153940800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:153938800-153941000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:153938800-153941000	Active TSS	Fetal Brain Female	brain
7	chr1:153938800-153941200	Active TSS	K562	blood
8	chr1:153938800-153941400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:153938800-153941600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:153939000-153940800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:153939000-153940800	Active TSS	NHDF-Ad	bronchial
12	chr1:153939000-153941000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:153939000-153941000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:153939000-153941200	Active TSS	Fetal Kidney	kidney
15	chr1:153939200-153940800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:153939200-153940800	Active TSS	Aorta	Aorta
17	chr1:153939200-153940800	Active TSS	Fetal Stomach	stomach
18	chr1:153939200-153940800	Active TSS	Psoas Muscle	Psoas
19	chr1:153939200-153940800	Active TSS	Right Ventricle	heart
20	chr1:153939200-153941000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr1:153939200-153941000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:153939200-153941000	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:153939200-153941000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:153939200-153941000	Active TSS	Fetal Brain Male	brain
25	chr1:153939200-153941200	Active TSS	Brain Germinal Matrix	brain
26	chr1:153939200-153941200	Active TSS	Ovary	ovary
27	chr1:153939200-153941400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:153939200-153941400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:153939400-153940800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:153939400-153940800	Active TSS	Primary T cells from cord blood	blood
31	chr1:153939400-153940800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:153939400-153940800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:153939400-153940800	Active TSS	Left Ventricle	heart
34	chr1:153939400-153941000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:153939400-153941000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:153939400-153941000	Active TSS	Colon Smooth Muscle	Colon
37	chr1:153939400-153941000	Active TSS	Fetal Intestine Large	intestine
38	chr1:153939400-153941000	Active TSS	Stomach Mucosa	stomach
39	chr1:153939400-153941200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:153939400-153941200	Active TSS	HepG2	liver
41	chr1:153939400-153941200	Active TSS	HSMMtube	muscle
42	chr1:153939400-153941400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:153939400-153941400	Active TSS	Osteobl	bone
44	chr1:153939400-153941600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:153939400-153941800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153939400-153942000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:153939600-153940800	Active TSS	Brain Angular Gyrus	brain
48	chr1:153939600-153940800	Active TSS	Fetal Heart	heart
49	chr1:153939600-153940800	Active TSS	Pancreas	Pancrea
50	chr1:153939600-153940800	Active TSS	NHLF	lung

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