Variant report

Variant	rs3130843
Chromosome Location	chr6:28908214-28908215
allele	A/T
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	SIN3AK20	chr6:28907994-28908538	H1-hESC	embryonic stem cell:	n/a	n/a
2	STAT3	chr6:28907916-28908395	MCF10A-Er-Src	breast:	n/a	chr6:28908171-28908179 chr6:28908169-28908180
3	MAX	chr6:28907738-28909821	HCT-116	colon:	n/a	n/a
4	SP1	chr6:28907906-28908518	H1-hESC	embryonic stem cell:	n/a	chr6:28908137-28908151 chr6:28908140-28908152 chr6:28908141-28908150
5	MYC	chr6:28907422-28909659	K562	blood:	n/a	n/a
6	CTBP2	chr6:28908143-28909186	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:28908084-28908502	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUND	chr6:28908050-28909126	H1-hESC	embryonic stem cell:	n/a	chr6:28908663-28908671 chr6:28908662-28908672 chr6:28908661-28908673
9	TCF12	chr6:28907813-28909791	A549	lung:	n/a	n/a
10	TEAD4	chr6:28908002-28909129	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:28908006-28908677	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr6:28908136-28908250	MCF-7	breast:	n/a	n/a
13	CBX3	chr6:28908169-28909746	K562	blood:	n/a	n/a
14	TEAD4	chr6:28907159-28910093	K562	blood:	n/a	n/a
15	CEBPB	chr6:28906922-28908259	Hela-S3	cervix:	n/a	n/a
16	ZNF143	chr6:28908176-28908953	GM12878	blood:	n/a	chr6:28908590-28908599
17	SIN3AK20	chr6:28907789-28909007	H1-hESC	embryonic stem cell:	n/a	n/a
18	TEAD4	chr6:28908031-28908423	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr6:28907782-28910012	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr6:28908148-28908342	K562	blood:	n/a	n/a
21	ATF3	chr6:28907986-28909765	HCT-116	colon:	n/a	n/a
22	GATA3	chr6:28907926-28908369	T-47D	breast:	n/a	n/a
23	SMC3	chr6:28907322-28908345	Hela-S3	cervix:	n/a	n/a
24	TBL1XR1	chr6:28908095-28909831	GM12878	blood:	n/a	n/a
25	GTF3C2	chr6:28907094-28909901	Hela-S3	cervix:	n/a	n/a
26	MAX	chr6:28908024-28909658	A549	lung:	n/a	n/a
27	ATF3	chr6:28908091-28909866	A549	lung:	n/a	n/a
28	RELA	chr6:28908182-28909569	GM19099	blood:	n/a	n/a
29	ZNF263	chr6:28908096-28909474	HEK293-T-REx	kidney:	n/a	n/a
30	MAX	chr6:28907752-28909629	NB4	blood:	n/a	n/a
31	JUND	chr6:28907300-28909628	K562	blood:	n/a	chr6:28908663-28908671 chr6:28908662-28908672 chr6:28908661-28908673
32	BHLHE40	chr6:28908212-28909730	K562	blood:	n/a	n/a
33	MAX	chr6:28908108-28909514	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr6:28908200-28908350	HBMEC	blood vessel:	n/a	n/a
35	MYBL2	chr6:28907979-28909704	HepG2	liver:	n/a	n/a
36	MTA3	chr6:28908202-28909640	GM12878	blood:	n/a	n/a
37	ATF2	chr6:28908185-28909707	H1-hESC	embryonic stem cell:	n/a	n/a
38	NR2F2	chr6:28907111-28909897	K562	blood:	n/a	n/a
39	TAF1	chr6:28908074-28908633	H1-hESC	embryonic stem cell:	n/a	n/a
40	TEAD4	chr6:28907626-28909719	K562	blood:	n/a	n/a
41	REST	chr6:28907610-28909793	H1-neurons	neurons:	n/a	n/a
42	STAT3	chr6:28907726-28908314	MCF10A-Er-Src	breast:	n/a	chr6:28908171-28908179 chr6:28908169-28908180
43	SP1	chr6:28907847-28908590	H1-hESC	embryonic stem cell:	n/a	chr6:28908137-28908151 chr6:28908140-28908152 chr6:28908141-28908150
44	HDAC2	chr6:28908190-28908704	H1-hESC	embryonic stem cell:	n/a	chr6:28908202-28908221
45	MAFK	chr6:28907866-28909536	K562	blood:	n/a	chr6:28908218-28908233
46	STAT3	chr6:28907752-28908313	MCF10A-Er-Src	breast:	n/a	chr6:28908171-28908179 chr6:28908169-28908180
47	POLR2A	chr6:28907824-28908377	HCT-116	colon:	n/a	n/a
48	SIN3AK20	chr6:28908063-28908465	SK-N-SH	brain:	n/a	n/a
49	CEBPB	chr6:28908166-28909737	GM12878	blood:	n/a	n/a
50	STAT5A	chr6:28908069-28909669	GM12878	blood:	n/a	chr6:28909313-28909324 chr6:28908712-28908720 chr6:28908171-28908179

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28863888..28865643-chr6:28906891..28908476,2	MCF-7	breast:
4	chr6:28856688..28858917-chr6:28907185..28909608,2	K562	blood:
5	chr6:28694415..28696951-chr6:28906885..28909854,2	K562	blood:
6	chr6:28806425..28808572-chr6:28907026..28910761,3	K562	blood:
7	chr6:28906950..28909090-chr6:28957555..28960455,2	K562	blood:
8	chr6:28906972..28909678-chr6:28910352..28912254,2	MCF-7	breast:
9	chr6:28899297..28900909-chr6:28906173..28908577,2	MCF-7	breast:
10	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
11	chr6:28846715..28849076-chr6:28906590..28908928,2	K562	blood:
12	chr6:28907315..28909915-chr6:28920300..28923261,2	MCF-7	breast:
13	chr6:28907996..28910654-chr6:28948439..28951310,2	MCF-7	breast:
14	chr6:28907069..28909532-chr6:28910998..28913070,2	K562	blood:
15	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
16	chr6:28844035..28846398-chr6:28907604..28909519,2	K562	blood:
17	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
18	chr6:28803772..28806116-chr6:28907591..28909225,2	K562	blood:

Variant related genes	Relation type
C6orf100	TF binding region
ENSG00000224157	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000263426	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1061625	0.89[ASN][1000 genomes]
rs1794588	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209127	0.88[ASN][1000 genomes]
rs209140	0.81[ASN][1000 genomes]
rs209147	0.80[ASN][1000 genomes]
rs2097424	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2765229	0.81[AFR][1000 genomes]
rs2894066	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131067	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131098	0.80[EUR][1000 genomes]
rs3132377	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3132380	0.84[ASN][1000 genomes]
rs6912843	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6926892	0.82[ASN][1000 genomes]
rs7740125	0.89[ASN][1000 genomes]
rs876737	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257395	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9257399	0.90[ASN][1000 genomes]
rs9257412	0.84[ASN][1000 genomes]
rs9257416	0.91[ASN][1000 genomes]
rs9257425	0.88[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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907200-28910000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:28907200-28910000	Active TSS	K562	blood
4	chr6:28907400-28909400	Active TSS	Placenta	Placenta
5	chr6:28907400-28909600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:28907400-28909600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:28907400-28909800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:28907400-28909800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28907400-28909800	Active TSS	GM12878-XiMat	blood
10	chr6:28907400-28909800	Active TSS	Hela-S3	cervix
11	chr6:28907400-28910000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:28907400-28910000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28907400-28910000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:28907400-28910000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:28907400-28910000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:28907400-28910200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:28907400-28910200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr6:28907400-28910200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:28907400-28910200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:28907400-28910200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:28907400-28910200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:28907400-28910200	Active TSS	Psoas Muscle	Psoas
23	chr6:28907400-28912400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:28907400-28912400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr6:28907400-28912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr6:28907400-28912400	Active TSS	A549	lung
27	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:28907600-28909000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr6:28907600-28909400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:28907600-28909800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr6:28907600-28910000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:28907600-28910000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:28907600-28910200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:28907600-28910200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:28907600-28910200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr6:28907600-28910200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr6:28907800-28908400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr6:28907800-28908400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr6:28907800-28908400	Active TSS	Fetal Brain Female	brain
41	chr6:28907800-28908400	Flanking Active TSS	NH-A	brain
42	chr6:28907800-28908600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:28907800-28908600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:28907800-28908600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr6:28907800-28908600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr6:28907800-28908600	Flanking Active TSS	HUVEC	blood vessel
47	chr6:28907800-28908800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr6:28907800-28908800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:28907800-28908800	Flanking Active TSS	Liver	Liver
50	chr6:28907800-28909000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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