Variant report

Variant	rs3806233
Chromosome Location	chr1:153600778-153600779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:94)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:94 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr1:153600720-153600995	K562	blood:	n/a	n/a
2	CTCF	chr1:153600660-153600810	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:153600700-153600850	HPAF	blood vessel:	n/a	n/a
4	MYC	chr1:153600705-153600916	K562	blood:	n/a	n/a
5	POLR2A	chr1:153600660-153601128	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:153600583-153601986	HepG2	liver:	n/a	n/a
7	CTCF	chr1:153600680-153600830	RPTEC	kidney:	n/a	n/a
8	ZBTB7A	chr1:153600683-153601062	K562	blood:	n/a	n/a
9	CTCF	chr1:153600677-153600859	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPD	chr1:153600688-153601065	HepG2	liver:	n/a	n/a
11	RCOR1	chr1:153599395-153600874	HepG2	liver:	n/a	n/a
12	CTCF	chr1:153600683-153600864	HepG2	liver:	n/a	n/a
13	HEY1	chr1:153600664-153601162	HepG2	liver:	n/a	n/a
14	CTCF	chr1:153600734-153600808	Gliobla	brain:	n/a	n/a
15	CTCF	chr1:153600700-153600850	HCPEpiC	choroid plexus:	n/a	n/a
16	CTCF	chr1:153600720-153600870	HepG2	liver:	n/a	n/a
17	CTCF	chr1:153600660-153600810	HUVEC	blood vessel:	n/a	n/a
18	HCFC1	chr1:153600614-153600920	K562	blood:	n/a	n/a
19	CTCF	chr1:153600708-153600868	NHEK	skin:	n/a	n/a
20	CTCF	chr1:153600751-153600817	MCF-7	breast:	n/a	n/a
21	CTCF	chr1:153600700-153600850	NB4	blood:	n/a	n/a
22	RAD21	chr1:153600656-153600912	HepG2	liver:	n/a	n/a
23	NR2F2	chr1:153599229-153600860	K562	blood:	n/a	n/a
24	CTCF	chr1:153600704-153600873	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:153600660-153600810	GM12874	blood:	n/a	n/a
26	CTCF	chr1:153599255-153600894	A549	lung:	n/a	n/a
27	CTCF	chr1:153600700-153600850	K562	blood:	n/a	n/a
28	ZNF263	chr1:153599392-153601314	HEK293-T-REx	kidney:	n/a	chr1:153600008-153600029
29	YY1	chr1:153600540-153601115	HepG2	liver:	n/a	n/a
30	RAD21	chr1:153600606-153600869	K562	blood:	n/a	n/a
31	CTCF	chr1:153600631-153600865	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr1:153600660-153600810	NHLF	lung:	n/a	n/a
33	MAZ	chr1:153600594-153600987	HepG2	liver:	n/a	n/a
34	CTCF	chr1:153600680-153600830	HRPEpiC	eye:	n/a	n/a
35	TBL1XR1	chr1:153600610-153600782	K562	blood:	n/a	n/a
36	CTCF	chr1:153600700-153600850	HFF-Myc	foreskin:	n/a	n/a
37	POLR2A	chr1:153600455-153601470	K562	blood:	n/a	n/a
38	POLR2A	chr1:153600561-153602432	HepG2	liver:	n/a	n/a
39	MYC	chr1:153600747-153600811	K562	blood:	n/a	n/a
40	RAD21	chr1:153600626-153601006	HepG2	liver:	n/a	n/a
41	CTCF	chr1:153600680-153600830	HBMEC	blood vessel:	n/a	n/a
42	CTCF	chr1:153600700-153600850	HCFaa	heart:	n/a	n/a
43	POLR2A	chr1:153600484-153601541	K562	blood:	n/a	n/a
44	MYC	chr1:153600618-153600982	K562	blood:	n/a	n/a
45	CTCF	chr1:153600726-153600835	MCF-7	breast:	n/a	n/a
46	MAZ	chr1:153600720-153600875	Hela-S3	cervix:	n/a	n/a
47	ZNF143	chr1:153600657-153600831	K562	blood:	n/a	n/a
48	POLR2A	chr1:153600729-153601082	HepG2	liver:	n/a	n/a
49	CTCF	chr1:153600720-153600870	HRE	kidney:	n/a	n/a
50	CTCF	chr1:153600660-153600810	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153600762-153600812	AG10803	skin:	n/a
2	chr1:153600762-153600812	NB4	blood:	n/a
3	chr1:153600762-153600812	HepG2	liver:	n/a
4	chr1:153600762-153600812	HAEpiC	amniotic membrane:	n/a
5	chr1:153600762-153600812	HMEC	breast:	n/a
6	chr1:153600762-153600812	GM06990	blood:	n/a
7	chr1:153600762-153600812	HRCEpiC	kidney:	n/a
8	chr1:153600762-153600812	A549	lung:	n/a
9	chr1:153600762-153600812	ECC-1	luminal epithelium:	n/a
10	chr1:153600762-153600812	HCF	heart:	n/a
11	chr1:153600762-153600812	AG09319	gingival:	n/a
12	chr1:153600762-153600812	SK-N-SH_RA	brain:	n/a
13	chr1:153600762-153600812	HCM	heart:	n/a
14	chr1:153600762-153600812	GM12878	blood:	n/a
15	chr1:153600762-153600812	HPAEpiC	pulmonary alveolar:	n/a
16	chr1:153600762-153600812	AG04449	skin:	fetal
17	chr1:153600762-153600812	Hela-S3	cervix:	n/a
18	chr1:153600762-153600812	H1-hESC	embryonic stem cell:	embryo
19	chr1:153600762-153600812	RPTEC	kidney:	n/a
20	chr1:153600762-153600812	SK-N-SH	brain:	n/a
21	chr1:153600762-153600812	HRE	kidney:	n/a
22	chr1:153600762-153600812	SAEC	small airway:	n/a
23	chr1:153600762-153600812	IMR90	lung:	fetal
24	chr1:153600762-153600812	ProgFib	skin:	n/a
25	chr1:153600762-153600812	HL-60	blood:	n/a
26	chr1:153600762-153600812	NHBE	bronchial:	n/a
27	chr1:153600762-153600812	Hepatocyte	liver:	n/a
28	chr1:153600762-153600812	HUVEC	blood vessel:	n/a
29	chr1:153600762-153600812	GM19239	blood:	n/a
30	chr1:153600762-153600812	NH-A	brain:	n/a
31	chr1:153600762-153600812	HEEpiC	esophagus:	n/a
32	chr1:153600762-153600812	PrEC	prostate:	n/a
33	chr1:153600762-153600812	AG04450	lung:	fetal
34	chr1:153600762-153600812	CMK	blood:	n/a
35	chr1:153600762-153600812	HNPCEpiC	eye:	n/a
36	chr1:153600762-153600812	SK-N-MC	brain:	n/a
37	chr1:153600762-153600812	K562	blood:	n/a
38	chr1:153600762-153600812	SKMC	muscle:	n/a
39	chr1:153600762-153600812	LNCaP	prostate:	n/a
40	chr1:153600762-153600812	HRPEpiC	eye:	n/a
41	chr1:153600762-153600812	HCPEpiC	choroid plexus:	n/a
42	chr1:153600762-153600812	HEK293	kidney:	embryo
43	chr1:153600762-153600812	MCF-7	breast:	n/a
44	chr1:153600762-153600812	AoSMC	blood vessel:	n/a
45	chr1:153600762-153600812	BE2_C	brain:	n/a
46	chr1:153600762-153600812	NT2-D1	testis:	n/a
47	chr1:153600762-153600812	Caco-2	colon:	n/a
48	chr1:153600762-153600812	U87	brain:	n/a
49	chr1:153600762-153600812	PFSK-1	brain:	n/a
50	chr1:153600762-153600812	PANC-1	pancreas:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153599949..153601639-chr1:153935071..153937718,2	MCF-7	breast:
2	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
3	chr1:153598208..153601029-chr1:153962097..153964477,2	K562	blood:
4	chr1:153599788..153602388-chr1:153699187..153702024,4	MCF-7	breast:
5	chr1:153599101..153601090-chr1:153642486..153644716,4	MCF-7	breast:
6	chr1:153515275..153518447-chr1:153598676..153601896,4	MCF-7	breast:
7	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
8	chr1:153597855..153601076-chr1:153629883..153633781,4	MCF-7	breast:
9	chr1:153508608..153510769-chr1:153600428..153603319,2	K562	blood:
10	chr1:153599605..153601359-chr1:153938449..153940087,2	MCF-7	breast:
11	chr1:153537634..153542525-chr1:153598837..153602183,9	K562	blood:
12	chr1:153599154..153601344-chr1:153747056..153749212,2	MCF-7	breast:
13	chr1:153598392..153603036-chr1:153933813..153937554,5	MCF-7	breast:
14	chr1:153599607..153601795-chr12:120727965..120730762,2	MCF-7	breast:

No data

Variant related genes	Relation type
S100A1	TF binding region
S100A13	TF binding region
S100A1	CpG island
S100A13	CpG island
ENSG00000143621	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10797056	0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs10797096	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10908746	0.80[ASN][1000 genomes]
rs10908848	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11265625	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1128894	0.80[ASN][1000 genomes]
rs11497739	0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11548102	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11548103	0.90[ASN][1000 genomes]
rs11548104	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11588347	0.85[EUR][1000 genomes]
rs12139953	0.83[EUR][1000 genomes]
rs12564925	0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs12730186	0.86[EUR][1000 genomes]
rs1888115	0.93[CHD][hapmap]
rs2274739	0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs2274740	0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs28379831	0.80[ASN][1000 genomes]
rs28380060	0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs28416529	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs28518786	0.89[EUR][1000 genomes]
rs28580554	0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs28700217	0.81[ASN][1000 genomes]
rs28754733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35760493	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3790411	0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs3790412	0.93[CHD][hapmap]
rs3795396	0.83[CHD][hapmap]
rs3806234	0.83[CHD][hapmap]
rs3818632	0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs3828031	0.93[CHD][hapmap]
rs3862047	0.88[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4072425	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4515830	0.92[CEU][hapmap]
rs4845557	0.80[ASN][1000 genomes]
rs4845563	0.88[CEU][hapmap];0.83[CHD][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs4845564	0.85[EUR][1000 genomes]
rs55772653	0.85[EUR][1000 genomes]
rs66721814	0.86[EUR][1000 genomes]
rs6674929	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7345	0.86[CHD][hapmap]
rs7934	0.93[CHD][hapmap]
rs913860	0.90[CHD][hapmap]
rs913861	0.83[CHD][hapmap]
rs9330298	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9330299	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9330300	0.88[ASN][1000 genomes]
rs9330301	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9660679	0.88[ASN][1000 genomes]
rs9662664	0.85[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9699949	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9700179	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9700928	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9726753	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9729773	0.91[ASN][1000 genomes]
rs9792913	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9792963	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9792967	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9793310	0.88[ASN][1000 genomes]
rs999418	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3806233	S100A13	cis	lymphoblastoid	seeQTL
rs3806233	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs3806233	S100A2	cis	cerebellum	SCAN
rs3806233	FLG	cis	cerebellum	SCAN
rs3806233	S100A13	cis	multi-tissue	Pritchard
rs3806233	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs3806233	S100A9	cis	parietal	SCAN
rs3806233	S100A10	cis	cerebellum	SCAN
rs3806233	S100A13	cis	parietal	SCAN
rs3806233	DCST2	cis	parietal	SCAN
rs3806233	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs3806233	SLC27A3	cis	cerebellum	SCAN
rs3806233	S100A16	cis	cerebellum	SCAN
rs3806233	S100A16	cis	parietal	SCAN
rs3806233	CHTOP	cis	Muscle Skeletal	GTEx
rs3806233	CTSS	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153597800-153600800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr1:153598200-153603600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr1:153598600-153601800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:153598800-153601400	Flanking Active TSS	Brain Hippocampus Middle	brain
5	chr1:153598800-153601400	Flanking Active TSS	K562	blood
6	chr1:153598800-153602200	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr1:153598800-153602400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:153599400-153600800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:153599600-153600800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:153599600-153600800	Weak transcription	Spleen	Spleen
11	chr1:153600000-153600800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:153600000-153600800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:153600000-153601000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153600000-153601000	Weak transcription	Psoas Muscle	Psoas
15	chr1:153600000-153601600	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:153600000-153601800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:153600000-153602600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:153600000-153602600	Enhancers	Fetal Thymus	thymus
19	chr1:153600000-153603200	Enhancers	Lung	lung
20	chr1:153600000-153604200	Enhancers	Fetal Heart	heart
21	chr1:153600000-153605600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:153600000-153605800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:153600000-153605800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:153600000-153605800	Weak transcription	Thymus	Thymus
25	chr1:153600000-153606600	Weak transcription	Aorta	Aorta
26	chr1:153600200-153600800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:153600200-153600800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:153600200-153600800	Enhancers	Left Ventricle	heart
29	chr1:153600200-153600800	Enhancers	Pancreas	Pancrea
30	chr1:153600200-153600800	Enhancers	Right Ventricle	heart
31	chr1:153600200-153600800	Enhancers	Stomach Mucosa	stomach
32	chr1:153600200-153600800	Flanking Active TSS	HepG2	liver
33	chr1:153600200-153601000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:153600200-153601000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:153600200-153601200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr1:153600200-153601200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:153600200-153601200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:153600200-153601200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:153600200-153601200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:153600200-153601600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:153600200-153602000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:153600200-153602200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:153600200-153602200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:153600200-153602600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:153600200-153602600	Weak transcription	Gastric	stomach
46	chr1:153600200-153603000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:153600200-153603200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:153600200-153603200	Enhancers	Adipose Nuclei	Adipose
49	chr1:153600200-153603400	Weak transcription	Liver	Liver
50	chr1:153600200-153603600	Enhancers	Fetal Stomach	stomach

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