Variant report

Variant	rs3218804
Chromosome Location	chr6:30875603-30875604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:389)
CpG islands
(count:183)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:389 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr6:30875535-30876082	A549	lung:	n/a	n/a
2	POLR2A	chr6:30875471-30876159	HL-60	blood:	n/a	n/a
3	PAX5	chr6:30875504-30875906	GM12892	blood:	n/a	n/a
4	MXI1	chr6:30875380-30876608	IMR90	lung:	n/a	n/a
5	MAX	chr6:30875495-30876402	MCF-7	breast:	n/a	n/a
6	ELF1	chr6:30875577-30876087	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:30875516-30876357	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr6:30875552-30876353	K562	blood:	n/a	n/a
9	POLR2A	chr6:30875499-30876256	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:30875472-30876384	Raji	blood:	n/a	n/a
11	ZNF143	chr6:30875491-30876340	K562	blood:	n/a	chr6:30875924-30875939 chr6:30875845-30875864 chr6:30875865-30875874 chr6:30875921-30875940 chr6:30875858-30875876 chr6:30875936-30875946 chr6:30875917-30875935 chr6:30875867-30875876
12	FOS	chr6:30875416-30876032	MCF10A-Er-Src	breast:	n/a	chr6:30875712-30875721
13	RCOR1	chr6:30875404-30876219	K562	blood:	n/a	n/a
14	IRF1	chr6:30875568-30876130	K562	blood:	n/a	chr6:30875707-30875721
15	POLR2A	chr6:30875527-30875865	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:30875545-30875817	HepG2	liver:	n/a	n/a
17	TBP	chr6:30875591-30876068	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFATC1	chr6:30875488-30876176	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:30875362-30876178	PANC-1	pancreas:	n/a	n/a
20	BCLAF1	chr6:30875469-30876244	K562	blood:	n/a	n/a
21	WRNIP1	chr6:30875598-30876071	GM12878	blood:	n/a	n/a
22	STAT5A	chr6:30875518-30876334	GM12878	blood:	n/a	n/a
23	GTF2B	chr6:30875548-30876158	K562	blood:	n/a	n/a
24	POU2F2	chr6:30875512-30876116	GM12878	blood:	n/a	n/a
25	ETS1	chr6:30875522-30876052	K562	blood:	n/a	chr6:30875864-30875877
26	IRF1	chr6:30875588-30876217	K562	blood:	n/a	chr6:30875707-30875721
27	MBD4	chr6:30875480-30876336	HepG2	liver:	n/a	n/a
28	FOS	chr6:30875464-30875976	MCF10A-Er-Src	breast:	n/a	chr6:30875712-30875721
29	E2F6	chr6:30875502-30876123	H1-hESC	embryonic stem cell:	n/a	chr6:30875714-30875725
30	POLR2A	chr6:30875586-30875829	GM12891	blood:	n/a	n/a
31	STAT3	chr6:30875532-30876024	MCF10A-Er-Src	breast:	n/a	n/a
32	MAFK	chr6:30875603-30876028	Hela-S3	cervix:	n/a	n/a
33	SPI1	chr6:30875594-30875946	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:30875486-30876135	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr6:30875407-30875999	GM12892	blood:	n/a	n/a
36	IRF4	chr6:30875514-30876088	GM12878	blood:	n/a	n/a
37	YY1	chr6:30875532-30876048	K562	blood:	n/a	n/a
38	CTCF	chr6:30875540-30875690	SK-N-SH_RA	brain:	n/a	n/a
39	TAF1	chr6:30875576-30875983	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr6:30875580-30875730	HCPEpiC	choroid plexus:	n/a	n/a
41	FOXP2	chr6:30875521-30875963	PFSK-1	brain:	n/a	n/a
42	SIN3AK20	chr6:30875495-30876124	SK-N-SH	brain:	n/a	n/a
43	GABPA	chr6:30875585-30876059	GM12878	blood:	n/a	chr6:30875935-30875944
44	RUNX3	chr6:30875432-30876204	GM12878	blood:	n/a	n/a
45	TEAD4	chr6:30875365-30876526	K562	blood:	n/a	n/a
46	FOS	chr6:30875407-30876024	MCF10A-Er-Src	breast:	n/a	chr6:30875712-30875721
47	YY1	chr6:30875540-30876311	SK-N-SH	brain:	n/a	n/a
48	NR2F2	chr6:30875067-30876554	K562	blood:	n/a	n/a
49	ZMIZ1	chr6:30875530-30876141	K562	blood:	n/a	n/a
50	MYC	chr6:30875580-30876102	MCF10A-Er-Src	breast:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30875586-30875636	SKMC	muscle:	n/a
2	chr6:30875592-30875642	Caco-2	colon:	n/a
3	chr6:30875586-30875636	NH-A	brain:	n/a
4	chr6:30875588-30875638	IMR90	lung:	fetal
5	chr6:30875588-30875638	Caco-2	colon:	n/a
6	chr6:30875588-30875638	HAEpiC	amniotic membrane:	n/a
7	chr6:30875588-30875638	K562	blood:	n/a
8	chr6:30875586-30875636	SK-N-SH_RA	brain:	n/a
9	chr6:30875592-30875642	AoSMC	blood vessel:	n/a
10	chr6:30875588-30875638	SK-N-SH_RA	brain:	n/a
11	chr6:30875588-30875638	HCM	heart:	n/a
12	chr6:30875592-30875642	Jurkat	blood:	n/a
13	chr6:30875586-30875636	GM19239	blood:	n/a
14	chr6:30875586-30875636	RPTEC	kidney:	n/a
15	chr6:30875588-30875638	AoSMC	blood vessel:	n/a
16	chr6:30875588-30875638	A549	lung:	n/a
17	chr6:30875586-30875636	T-47D	breast:	n/a
18	chr6:30875586-30875636	MCF-7	breast:	n/a
19	chr6:30875592-30875642	AG09309	skin:	n/a
20	chr6:30875588-30875638	NT2-D1	testis:	n/a
21	chr6:30875592-30875642	PFSK-1	brain:	n/a
22	chr6:30875592-30875642	SKMC	muscle:	n/a
23	chr6:30875592-30875642	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:30875588-30875638	CMK	blood:	n/a
25	chr6:30875592-30875642	ovcar-3	ovarian:	n/a
26	chr6:30875586-30875636	U87	brain:	n/a
27	chr6:30875588-30875638	GM12892	blood:	n/a
28	chr6:30875586-30875636	Hepatocyte	liver:	n/a
29	chr6:30875592-30875642	AG04450	lung:	fetal
30	chr6:30875588-30875638	SK-N-MC	brain:	n/a
31	chr6:30875592-30875642	GM12892	blood:	n/a
32	chr6:30875588-30875638	SAEC	small airway:	n/a
33	chr6:30875586-30875636	HUVEC	blood vessel:	n/a
34	chr6:30875586-30875636	NT2-D1	testis:	n/a
35	chr6:30875588-30875638	AG04449	skin:	fetal
36	chr6:30875592-30875642	GM12878	blood:	n/a
37	chr6:30875586-30875636	HRPEpiC	eye:	n/a
38	chr6:30875592-30875642	Hela-S3	cervix:	n/a
39	chr6:30875586-30875636	AG09309	skin:	n/a
40	chr6:30875592-30875642	SK-N-MC	brain:	n/a
41	chr6:30875586-30875636	HCF	heart:	n/a
42	chr6:30875592-30875642	NHBE	bronchial:	n/a
43	chr6:30875586-30875636	MCF10A-Er-Src	breast:	n/a
44	chr6:30875592-30875642	HUVEC	blood vessel:	n/a
45	chr6:30875592-30875642	BJ	skin:	n/a
46	chr6:30875588-30875638	HRCEpiC	kidney:	n/a
47	chr6:30875588-30875638	T-47D	breast:	n/a
48	chr6:30875592-30875642	IMR90	lung:	fetal
49	chr6:30875588-30875638	GM12891	blood:	n/a
50	chr6:30875592-30875642	RPTEC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:30849687..30852078-chr6:30875212..30877587,2	K562	blood:
2	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
3	chr6:30710580..30713200-chr6:30873655..30875872,3	K562	blood:
4	chr6:30856696..30860777-chr6:30873663..30877180,4	K562	blood:
5	chr6:30849765..30853673-chr6:30873635..30876591,7	MCF-7	breast:
6	chr6:30850512..30853465-chr6:30873614..30877587,4	K562	blood:
7	chr6:30687770..30690244-chr6:30875447..30877174,2	MCF-7	breast:
8	chr6:30848838..30854096-chr6:30874501..30878794,8	MCF-7	breast:
9	chr6:30862733..30867301-chr6:30870947..30877299,8	K562	blood:
10	chr6:30853891..30856446-chr6:30875282..30877202,3	K562	blood:
11	chr6:30521879..30524871-chr6:30874411..30877273,3	K562	blood:
12	chr6:30861872..30865234-chr6:30873633..30877003,5	MCF-7	breast:
13	chr6:30859072..30860642-chr6:30873697..30876648,2	MCF-7	breast:
14	chr6:30874031..30876407-chr6:30886352..30887855,2	MCF-7	breast:

No data

Variant related genes	Relation type
GTF2H4	TF binding region
VARS2	TF binding region
VARS2	CpG island
GTF2H4	CpG island
ENSG00000272273	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204590	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10947109	0.94[ASN][1000 genomes]
rs11759918	0.82[ASN][1000 genomes]
rs17189749	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17196123	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17840009	0.82[ASN][1000 genomes]
rs2894054	0.91[ASN][1000 genomes]
rs3218825	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs45627239	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55697712	0.94[ASN][1000 genomes]
rs59124304	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6926224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926723	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940037	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73727104	0.94[ASN][1000 genomes]
rs73727106	0.94[ASN][1000 genomes]
rs73727107	0.85[ASN][1000 genomes]
rs73727480	0.90[ASN][1000 genomes]
rs7747800	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761138	0.85[ASN][1000 genomes]
rs7770596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772269	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30858400-30876000	Weak transcription	Fetal Heart	heart
2	chr6:30866600-30876000	Weak transcription	Small Intestine	intestine
3	chr6:30867800-30876000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:30875000-30876600	Active TSS	GM12878-XiMat	blood
5	chr6:30875000-30877000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:30875200-30875800	Flanking Active TSS	Dnd41	blood
7	chr6:30875200-30876200	Active TSS	Primary T cells from cord blood	blood
8	chr6:30875200-30876200	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr6:30875200-30876200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr6:30875200-30876200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:30875200-30876200	Active TSS	Liver	Liver
12	chr6:30875200-30876200	Active TSS	Duodenum Mucosa	Duodenum
13	chr6:30875200-30876200	Active TSS	Placenta	Placenta
14	chr6:30875200-30876200	Active TSS	Thymus	Thymus
15	chr6:30875200-30876400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:30875200-30876400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:30875200-30876400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:30875200-30876400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:30875200-30876400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:30875200-30876400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:30875200-30876400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr6:30875200-30876400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr6:30875200-30876400	Active TSS	Fetal Intestine Large	intestine
24	chr6:30875200-30876400	Active TSS	Fetal Intestine Small	intestine
25	chr6:30875200-30876400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr6:30875200-30876400	Active TSS	Rectal Smooth Muscle	rectum
27	chr6:30875200-30876600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:30875200-30876600	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr6:30875200-30876600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:30875200-30876600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:30875200-30876600	Active TSS	Pancreas	Pancrea
32	chr6:30875200-30876600	Active TSS	A549	lung
33	chr6:30875200-30877000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:30875200-30877000	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr6:30875200-30877200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:30875200-30877200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr6:30875400-30875800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr6:30875400-30875800	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr6:30875400-30875800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr6:30875400-30875800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:30875400-30875800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:30875400-30875800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:30875400-30875800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr6:30875400-30875800	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr6:30875400-30875800	Flanking Active TSS	Fetal Thymus	thymus
46	chr6:30875400-30875800	Transcr. at gene 5' and 3'	Right Atrium	heart
47	chr6:30875400-30876000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:30875400-30876000	Active TSS	HepG2	liver
49	chr6:30875400-30876200	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:30875400-30876400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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