Variant report

Variant	rs7738979
Chromosome Location	chr6:28557312-28557313
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:223)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:223 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:28556995-28557561	A549	lung:	n/a	n/a
2	YY1	chr6:28557002-28557567	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr6:28556917-28557666	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr6:28557001-28557386	GM12878	blood:	n/a	n/a
5	TCF7L2	chr6:28557003-28557539	HCT-116	colon:	n/a	n/a
6	MAX	chr6:28557108-28557684	SK-N-SH	brain:	n/a	n/a
7	ZKSCAN1	chr6:28557004-28557602	Hela-S3	cervix:	n/a	n/a
8	TBP	chr6:28556918-28557456	H1-hESC	embryonic stem cell:	n/a	n/a
9	BHLHE40	chr6:28556999-28557493	HepG2	liver:	n/a	n/a
10	SIN3A	chr6:28556860-28558249	H1-hESC	embryonic stem cell:	n/a	n/a
11	ARID3A	chr6:28556957-28557603	HepG2	liver:	n/a	n/a
12	MAX	chr6:28557040-28557644	HepG2	liver:	n/a	n/a
13	RCOR1	chr6:28556973-28557589	HepG2	liver:	n/a	n/a
14	EBF1	chr6:28556955-28557365	GM12878	blood:	n/a	n/a
15	TBP	chr6:28556902-28557457	HepG2	liver:	n/a	n/a
16	MAX	chr6:28556965-28557732	ECC-1	luminal epithelium:	n/a	n/a
17	EP300	chr6:28557004-28557481	H1-hESC	embryonic stem cell:	n/a	n/a
18	HDAC2	chr6:28556919-28557617	HepG2	liver:	n/a	n/a
19	MYC	chr6:28557016-28557665	MCF10A-Er-Src	breast:	n/a	n/a
20	MAX	chr6:28556907-28557724	MCF-7	breast:	n/a	n/a
21	CEBPB	chr6:28557010-28557705	HepG2	liver:	n/a	n/a
22	HNF4A	chr6:28556983-28557444	HepG2	liver:	n/a	chr6:28557181-28557196
23	RXRA	chr6:28556984-28557461	HepG2	liver:	n/a	n/a
24	CREB1	chr6:28557111-28557360	A549	lung:	n/a	n/a
25	ELK1	chr6:28556974-28557439	Hela-S3	cervix:	n/a	n/a
26	HNF4G	chr6:28556828-28557443	HepG2	liver:	n/a	chr6:28557182-28557197
27	TCF7L2	chr6:28556960-28557752	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr6:28556950-28557584	H1-hESC	embryonic stem cell:	n/a	n/a
29	ATF2	chr6:28556906-28557795	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF7	chr6:28556963-28557693	H1-hESC	embryonic stem cell:	n/a	n/a
31	WRNIP1	chr6:28556999-28557484	GM12878	blood:	n/a	n/a
32	TAF1	chr6:28557004-28557483	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr6:28556886-28557690	HCT-116	colon:	n/a	n/a
34	MAZ	chr6:28557051-28557534	Hela-S3	cervix:	n/a	n/a
35	USF1	chr6:28557054-28557474	A549	lung:	n/a	n/a
36	CTCF	chr6:28557180-28557330	HepG2	liver:	n/a	n/a
37	REST	chr6:28557156-28557465	SK-N-SH	brain:	n/a	n/a
38	NFIC	chr6:28556958-28557602	HepG2	liver:	n/a	n/a
39	GATA3	chr6:28557004-28557680	MCF-7	breast:	n/a	n/a
40	ZBTB33	chr6:28556932-28557612	A549	lung:	n/a	n/a
41	TEAD4	chr6:28556939-28557558	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr6:28556991-28557623	H1-hESC	embryonic stem cell:	n/a	n/a
43	ETS1	chr6:28556984-28557601	A549	lung:	n/a	n/a
44	ETS1	chr6:28556905-28557742	A549	lung:	n/a	n/a
45	TBP	chr6:28556937-28557354	GM12878	blood:	n/a	n/a
46	MAFK	chr6:28556944-28557527	H1-hESC	embryonic stem cell:	n/a	n/a
47	SIN3AK20	chr6:28556737-28557835	MCF-7	breast:	n/a	n/a
48	RFX5	chr6:28556947-28557569	Hela-S3	cervix:	n/a	n/a
49	NR2F2	chr6:28556949-28557787	MCF-7	breast:	n/a	n/a
50	POLR2A	chr6:28556906-28557599	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28557283-28557333	HRCEpiC	kidney:	n/a
2	chr6:28557283-28557333	PFSK-1	brain:	n/a
3	chr6:28557291-28557341	GM19239	blood:	n/a
4	chr6:28557291-28557341	HEEpiC	esophagus:	n/a
5	chr6:28557291-28557341	NHBE	bronchial:	n/a
6	chr6:28557291-28557341	HMEC	breast:	n/a
7	chr6:28557283-28557333	HIPEpiC	eye:	n/a
8	chr6:28557283-28557333	Caco-2	colon:	n/a
9	chr6:28557291-28557341	SKMC	muscle:	n/a
10	chr6:28557291-28557341	HRE	kidney:	n/a
11	chr6:28557283-28557333	PrEC	prostate:	n/a
12	chr6:28557283-28557333	NHDF-neo	bronchial:	n/a
13	chr6:28557283-28557333	GM12892	blood:	n/a
14	chr6:28557283-28557333	T-47D	breast:	n/a
15	chr6:28557283-28557333	MCF-7	breast:	n/a
16	chr6:28557283-28557333	AG10803	skin:	n/a
17	chr6:28557283-28557333	ovcar-3	ovarian:	n/a
18	chr6:28557291-28557341	NT2-D1	testis:	n/a
19	chr6:28557291-28557341	Jurkat	blood:	n/a
20	chr6:28557291-28557341	HNPCEpiC	eye:	n/a
21	chr6:28557291-28557341	RPTEC	kidney:	n/a
22	chr6:28557283-28557333	CMK	blood:	n/a
23	chr6:28557291-28557341	MCF10A-Er-Src	breast:	n/a
24	chr6:28557283-28557333	K562	blood:	n/a
25	chr6:28557291-28557341	HPAEpiC	pulmonary alveolar:	n/a
26	chr6:28557283-28557333	NB4	blood:	n/a
27	chr6:28557291-28557341	H1-hESC	embryonic stem cell:	embryo
28	chr6:28557283-28557333	Hepatocyte	liver:	n/a
29	chr6:28557291-28557341	SK-N-MC	brain:	n/a
30	chr6:28557291-28557341	AoSMC	blood vessel:	n/a
31	chr6:28557291-28557341	PFSK-1	brain:	n/a
32	chr6:28557291-28557341	HL-60	blood:	n/a
33	chr6:28557291-28557341	A549	lung:	n/a
34	chr6:28557283-28557333	AoSMC	blood vessel:	n/a
35	chr6:28557283-28557333	SKMC	muscle:	n/a
36	chr6:28557291-28557341	HCF	heart:	n/a
37	chr6:28557283-28557333	HEK293	kidney:	embryo
38	chr6:28557283-28557333	A549	lung:	n/a
39	chr6:28557283-28557333	HAEpiC	amniotic membrane:	n/a
40	chr6:28557283-28557333	Hela-S3	cervix:	n/a
41	chr6:28557291-28557341	K562	blood:	n/a
42	chr6:28557283-28557333	GM19239	blood:	n/a
43	chr6:28557291-28557341	AG09309	skin:	n/a
44	chr6:28557283-28557333	HMEC	breast:	n/a
45	chr6:28557283-28557333	IMR90	lung:	fetal
46	chr6:28557291-28557341	LNCaP	prostate:	n/a
47	chr6:28557283-28557333	NT2-D1	testis:	n/a
48	chr6:28557291-28557341	HCPEpiC	choroid plexus:	n/a
49	chr6:28557291-28557341	GM06990	blood:	n/a
50	chr6:28557283-28557333	GM12878	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28556555..28559076-chr6:28582763..28585041,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPX5-1	chr6:28557006-28559524	XLOC_005223
2	lnc-SCAND3-2	chr6:28557137-28557480	NONHSAT108472

No data

Variant related genes	Relation type
SCAND3	TF binding region
SCAND3	CpG island
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11753292	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11754112	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11754599	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11757235	0.89[ASN][1000 genomes]
rs11758822	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12110753	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12111360	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1319076	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28382587	0.89[ASN][1000 genomes]
rs2893967	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34211304	0.89[ASN][1000 genomes]
rs34560199	0.89[ASN][1000 genomes]
rs34668037	0.89[ASN][1000 genomes]
rs3886843	0.89[ASN][1000 genomes]
rs4435933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56958518	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73391123	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73402976	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73402978	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73402982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73402983	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73404961	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73404965	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407134	0.88[AFR][1000 genomes]
rs73407157	0.92[AFR][1000 genomes]
rs73407159	0.92[AFR][1000 genomes]
rs73409121	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73409125	0.89[ASN][1000 genomes]
rs73409140	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7770993	0.88[AFR][1000 genomes]
rs7774808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][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:90 , 50 per page) page: 1 2

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	chr6:28553800-28557600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:28553800-28558200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:28553800-28558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:28553800-28558400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:28554000-28558000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
10	chr6:28554400-28558400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28554400-28558400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:28555600-28557400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:28555800-28557400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:28555800-28557400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:28555800-28557400	Weak transcription	Pancreas	Pancrea
16	chr6:28556000-28558000	Enhancers	HMEC	breast
17	chr6:28556000-28558200	Active TSS	Fetal Brain Female	brain
18	chr6:28556200-28558400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr6:28556400-28558200	Active TSS	A549	lung
20	chr6:28556600-28558000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:28556800-28557400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
22	chr6:28556800-28557400	Active TSS	NHLF	lung
23	chr6:28556800-28557600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:28556800-28557600	Active TSS	Muscle Satellite Cultured Cells	--
25	chr6:28556800-28557600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:28556800-28557600	Flanking Active TSS	GM12878-XiMat	blood
27	chr6:28556800-28557800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:28556800-28558000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:28556800-28558000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:28556800-28558000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
31	chr6:28556800-28558000	Active TSS	Brain Germinal Matrix	brain
32	chr6:28556800-28558000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28556800-28558000	Flanking Active TSS	NHEK	skin
34	chr6:28556800-28558200	Flanking Active TSS	Hela-S3	cervix
35	chr6:28556800-28558200	Active TSS	NH-A	brain
36	chr6:28556800-28558400	Active TSS	Fetal Brain Male	brain
37	chr6:28556800-28558400	Bivalent/Poised TSS	Fetal Kidney	kidney
38	chr6:28557000-28557400	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
39	chr6:28557000-28557400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:28557000-28557400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:28557000-28557400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:28557000-28557400	Active TSS	Fetal Lung	lung
43	chr6:28557000-28557400	Active TSS	HepG2	liver
44	chr6:28557000-28557400	Active TSS	HSMMtube	muscle
45	chr6:28557000-28557600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:28557000-28557600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
47	chr6:28557000-28557600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr6:28557000-28557600	Active TSS	Fetal Muscle Trunk	muscle
49	chr6:28557000-28557600	Active TSS	NHDF-Ad	bronchial
50	chr6:28557000-28557800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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