Variant report

Variant	rs411538
Chromosome Location	chr6:28555450-28555451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:28554599-28555512	HepG2	liver:	n/a	n/a
2	GABPA	chr6:28554621-28555627	A549	lung:	n/a	n/a
3	RCOR1	chr6:28554876-28555594	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:28554762-28555524	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr6:28554990-28555704	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr6:28554504-28555595	A549	lung:	n/a	n/a
7	MAFF	chr6:28555030-28555595	HepG2	liver:	n/a	n/a
8	SP2	chr6:28554777-28555518	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr6:28554924-28555549	SK-N-SH_RA	brain:	n/a	n/a
10	TCF12	chr6:28554626-28555485	A549	lung:	n/a	n/a
11	TEAD4	chr6:28554813-28555473	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:28554648-28555467	HepG2	liver:	n/a	n/a
13	MAX	chr6:28554695-28555520	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr6:28554829-28555474	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr6:28554935-28555497	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr6:28554935-28555519	HepG2	liver:	n/a	n/a
17	MAX	chr6:28554677-28555525	A549	lung:	n/a	n/a
18	USF2	chr6:28555230-28555603	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:28554718-28555463	Raji	blood:	n/a	n/a
20	POLR2A	chr6:28554760-28555524	HepG2	liver:	n/a	n/a
21	YY1	chr6:28554784-28555587	SK-N-SH_RA	brain:	n/a	n/a
22	YY1	chr6:28554875-28555496	GM12878	blood:	n/a	n/a
23	TAF1	chr6:28554822-28555716	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr6:28554727-28555499	Hela-S3	cervix:	n/a	n/a
25	GABPA	chr6:28554644-28555611	SK-N-SH	brain:	n/a	n/a
26	MXI1	chr6:28554510-28555533	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:28554767-28555697	SK-N-SH	brain:	n/a	n/a
28	YY1	chr6:28554974-28555557	H1-hESC	embryonic stem cell:	n/a	n/a
29	BCLAF1	chr6:28554832-28555485	GM12878	blood:	n/a	chr6:28555112-28555121
30	TAF7	chr6:28554737-28555457	H1-hESC	embryonic stem cell:	n/a	n/a
31	KAP1	chr6:28554761-28555589	U2OS	brain:	n/a	n/a
32	MAX	chr6:28554734-28555492	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIN3AK20	chr6:28554535-28555724	MCF-7	breast:	n/a	n/a
34	TAF1	chr6:28554659-28555468	A549	lung:	n/a	n/a
35	TAF1	chr6:28554628-28555492	ECC-1	luminal epithelium:	n/a	n/a
36	TAF1	chr6:28554667-28555541	H1-hESC	embryonic stem cell:	n/a	n/a
37	SP2	chr6:28554749-28555491	HepG2	liver:	n/a	n/a
38	MAX	chr6:28554661-28555607	ECC-1	luminal epithelium:	n/a	n/a
39	MYC	chr6:28554892-28555477	MCF10A-Er-Src	breast:	n/a	n/a
40	RUNX3	chr6:28554968-28555467	GM12878	blood:	n/a	n/a
41	YY1	chr6:28554762-28555532	HepG2	liver:	n/a	n/a
42	REST	chr6:28554600-28555498	A549	lung:	n/a	n/a
43	POLR2A	chr6:28554705-28555463	MCF-7	breast:	n/a	n/a
44	ELF1	chr6:28554776-28555471	MCF-7	breast:	n/a	n/a
45	MYBL2	chr6:28554692-28555528	HepG2	liver:	n/a	n/a
46	POLR2A	chr6:28554766-28555453	GM18951	blood:	n/a	n/a
47	YY1	chr6:28554957-28555562	A549	lung:	n/a	n/a
48	TAF1	chr6:28554620-28555662	H1-neurons	neurons:	n/a	n/a
49	RELA	chr6:28554500-28555495	GM19099	blood:	n/a	n/a
50	CHD1	chr6:28554783-28555556	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28555440-28555490	MCF10A-Er-Src	breast:	n/a
2	chr6:28555440-28555490	HCM	heart:	n/a
3	chr6:28555440-28555490	NB4	blood:	n/a
4	chr6:28555440-28555490	CMK	blood:	n/a
5	chr6:28555440-28555490	MCF-7	breast:	n/a
6	chr6:28555440-28555490	HMEC	breast:	n/a
7	chr6:28555440-28555490	HRE	kidney:	n/a
8	chr6:28555440-28555490	AG09309	skin:	n/a
9	chr6:28555440-28555490	HCT-116	colon:	n/a
10	chr6:28555440-28555490	PANC-1	pancreas:	n/a
11	chr6:28555440-28555490	RPTEC	kidney:	n/a
12	chr6:28555440-28555490	Hepatocyte	liver:	n/a
13	chr6:28555440-28555490	NHBE	bronchial:	n/a
14	chr6:28555440-28555490	NT2-D1	testis:	n/a
15	chr6:28555440-28555490	SK-N-SH_RA	brain:	n/a
16	chr6:28555440-28555490	HEEpiC	esophagus:	n/a
17	chr6:28555440-28555490	Caco-2	colon:	n/a
18	chr6:28555440-28555490	AoSMC	blood vessel:	n/a
19	chr6:28555440-28555490	HEK293	kidney:	embryo
20	chr6:28555440-28555490	HNPCEpiC	eye:	n/a
21	chr6:28555440-28555490	SKMC	muscle:	n/a
22	chr6:28555440-28555490	SAEC	small airway:	n/a
23	chr6:28555440-28555490	AG04449	skin:	fetal
24	chr6:28555440-28555490	U87	brain:	n/a
25	chr6:28555440-28555490	BE2_C	brain:	n/a
26	chr6:28555440-28555490	HRCEpiC	kidney:	n/a
27	chr6:28555440-28555490	GM06990	blood:	n/a
28	chr6:28555440-28555490	Jurkat	blood:	n/a
29	chr6:28555440-28555490	IMR90	lung:	fetal
30	chr6:28555440-28555490	AG10803	skin:	n/a
31	chr6:28555440-28555490	K562	blood:	n/a
32	chr6:28555440-28555490	T-47D	breast:	n/a
33	chr6:28555440-28555490	NH-A	brain:	n/a
34	chr6:28555440-28555490	PFSK-1	brain:	n/a
35	chr6:28555440-28555490	GM12878	blood:	n/a
36	chr6:28555440-28555490	HL-60	blood:	n/a
37	chr6:28555440-28555490	HCPEpiC	choroid plexus:	n/a
38	chr6:28555440-28555490	AG04450	lung:	fetal
39	chr6:28555440-28555490	NHDF-neo	bronchial:	n/a
40	chr6:28555440-28555490	AG09319	gingival:	n/a
41	chr6:28555440-28555490	PrEC	prostate:	n/a
42	chr6:28555440-28555490	GM19239	blood:	n/a
43	chr6:28555440-28555490	HCF	heart:	n/a
44	chr6:28555440-28555490	GM12891	blood:	n/a
45	chr6:28555440-28555490	Hela-S3	cervix:	n/a
46	chr6:28555440-28555490	HepG2	liver:	n/a
47	chr6:28555440-28555490	SK-N-SH	brain:	n/a
48	chr6:28555440-28555490	ovcar-3	ovarian:	n/a
49	chr6:28555440-28555490	HIPEpiC	eye:	n/a
50	chr6:28555440-28555490	ProgFib	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28456446..28459153-chr6:28555326..28557057,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPX5-1	chr6:28555155-28555509	XLOC_005223

No data

Variant related genes	Relation type
SCAND3	TF binding region
SCAND3	CpG island

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10080420	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10434846	1.00[ASN][1000 genomes]
rs10733177	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755647	1.00[ASN][1000 genomes]
rs10807032	1.00[ASN][1000 genomes]
rs10807036	0.83[ASN][1000 genomes]
rs10807040	1.00[ASN][1000 genomes]
rs11758055	1.00[ASN][1000 genomes]
rs12332986	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474986	0.94[ASN][1000 genomes]
rs2057295	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108924	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2191036	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2394119	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382606	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs34358978	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34931542	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs381493	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384399	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852211	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389603	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392471	0.88[ASN][1000 genomes]
rs394772	1.00[ASN][1000 genomes]
rs399558	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3999023	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402426	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404343	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408255	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121090	1.00[ASN][1000 genomes]
rs418628	1.00[ASN][1000 genomes]
rs418898	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420436	1.00[ASN][1000 genomes]
rs420463	1.00[ASN][1000 genomes]
rs422089	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs424426	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426922	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429875	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434636	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442174	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs443924	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449074	1.00[ASN][1000 genomes]
rs454746	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711176	1.00[ASN][1000 genomes]
rs4713172	1.00[ASN][1000 genomes]
rs4713174	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5007575	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs55860825	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456820	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6456829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456832	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456833	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6906826	1.00[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs6923163	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925972	1.00[ASN][1000 genomes]
rs6927023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6935589	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6937042	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6938371	1.00[EUR][1000 genomes]
rs6941222	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381746	1.00[ASN][1000 genomes]
rs7382159	1.00[ASN][1000 genomes]
rs7382309	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382583	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761914	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771490	1.00[ASN][1000 genomes]
rs7773193	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911177	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911178	0.88[ASN][1000 genomes]
rs9295770	1.00[EUR][1000 genomes]
rs9393922	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393923	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461457	1.00[EUR][1000 genomes]
rs9461464	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468375	1.00[EUR][1000 genomes]
rs9468384	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468394	1.00[ASN][1000 genomes]
rs9654587	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552400-28559600	Strong transcription	K562	blood
2	chr6:28553000-28558200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28553200-28558200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28553200-28558600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28553800-28556400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:28553800-28557600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28553800-28558200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28553800-28558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:28553800-28558400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:28554000-28555600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
11	chr6:28554000-28555600	Active TSS	Fetal Kidney	kidney
12	chr6:28554000-28555600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:28554000-28555600	Active TSS	Lung	lung
14	chr6:28554000-28555600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
15	chr6:28554000-28555800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:28554000-28555800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:28554000-28555800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
18	chr6:28554000-28556000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:28554000-28556000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
21	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:28554000-28558000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
23	chr6:28554200-28555600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
24	chr6:28554200-28555600	Active TSS	Rectal Smooth Muscle	rectum
25	chr6:28554200-28555800	Active TSS	Colonic Mucosa	Colon
26	chr6:28554200-28555800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
27	chr6:28554200-28555800	Bivalent/Poised TSS	Fetal Stomach	stomach
28	chr6:28554200-28555800	Bivalent/Poised TSS	HepG2	liver
29	chr6:28554200-28556000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:28554400-28555600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:28554400-28555600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr6:28554400-28555600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:28554400-28555600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:28554400-28555600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr6:28554400-28555600	Active TSS	Fetal Intestine Small	intestine
36	chr6:28554400-28555600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr6:28554400-28555600	Bivalent/Poised TSS	Left Ventricle	heart
38	chr6:28554400-28555600	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:28554400-28555800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:28554400-28555800	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
41	chr6:28554400-28555800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr6:28554400-28555800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
43	chr6:28554400-28555800	Active TSS	Right Ventricle	heart
44	chr6:28554400-28556000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:28554400-28556000	Active TSS	A549	lung
46	chr6:28554400-28558400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:28554400-28558400	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr6:28554600-28555600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:28554600-28555600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:28554600-28555600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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