Variant report

Variant	rs1225600
Chromosome Location	chr6:28237445-28237446
allele	C/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	SETDB1	chr6:28237256-28237619	U2OS	brain:	n/a	n/a
2	FOSL1	chr6:28237081-28237817	HCT-116	colon:	n/a	n/a
3	STAT3	chr6:28237337-28237617	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr6:28237115-28237746	SK-N-SH	brain:	n/a	n/a
5	MAFF	chr6:28237245-28237672	K562	blood:	n/a	chr6:28237426-28237444
6	EP300	chr6:28237279-28237582	SK-N-SH_RA	brain:	n/a	n/a
7	MAFK	chr6:28237318-28237652	H1-hESC	embryonic stem cell:	n/a	chr6:28237483-28237498
8	JUND	chr6:28237370-28237628	HepG2	liver:	n/a	chr6:28237482-28237493
9	CTCF	chr6:28237300-28237450	HBMEC	blood vessel:	n/a	n/a
10	FOSL2	chr6:28237263-28237614	HepG2	liver:	n/a	n/a
11	CTCF	chr6:28237320-28237470	AG09319	gingival:	n/a	n/a
12	STAT3	chr6:28237297-28237629	MCF10A-Er-Src	breast:	n/a	n/a
13	MAFK	chr6:28237256-28237668	HepG2	liver:	n/a	chr6:28237483-28237498
14	FOS	chr6:28237224-28237705	HUVEC	blood vessel:	n/a	chr6:28237482-28237493
15	MYC	chr6:28237388-28237560	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr6:28237318-28237602	MCF10A-Er-Src	breast:	n/a	n/a
17	JUND	chr6:28237233-28237782	SK-N-SH	brain:	n/a	chr6:28237482-28237493
18	ARID3A	chr6:28237306-28237462	K562	blood:	n/a	n/a
19	STAT3	chr6:28237341-28237630	MCF10A-Er-Src	breast:	n/a	n/a
20	EP300	chr6:28237323-28237604	K562	blood:	n/a	n/a
21	FOSL2	chr6:28237330-28237610	A549	lung:	n/a	n/a
22	ELF1	chr6:28237212-28237500	K562	blood:	n/a	n/a
23	CBX3	chr6:28237082-28237723	K562	blood:	n/a	n/a
24	JUN	chr6:28237267-28237660	HUVEC	blood vessel:	n/a	n/a
25	JUND	chr6:28237286-28237651	K562	blood:	n/a	chr6:28237482-28237493
26	ZNF143	chr6:28237351-28237562	K562	blood:	n/a	n/a
27	NFIC	chr6:28237117-28237724	SK-N-SH	brain:	n/a	n/a
28	FOS	chr6:28237189-28237675	MCF10A-Er-Src	breast:	n/a	chr6:28237482-28237493
29	EP300	chr6:28237331-28237607	Hela-S3	cervix:	n/a	n/a
30	ZMIZ1	chr6:28237386-28237568	K562	blood:	n/a	n/a
31	MAFF	chr6:28237280-28237650	HepG2	liver:	n/a	chr6:28237426-28237444
32	MYC	chr6:28237298-28237592	MCF10A-Er-Src	breast:	n/a	n/a
33	MAFK	chr6:28237302-28237658	HepG2	liver:	n/a	chr6:28237483-28237498
34	JUN	chr6:28236993-28237755	K562	blood:	n/a	n/a
35	POLR2A	chr6:28237399-28237566	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr6:28237116-28237784	HUVEC	blood vessel:	n/a	n/a
37	JUND	chr6:28237142-28237752	SK-N-SH	brain:	n/a	chr6:28237482-28237493
38	STAT3	chr6:28237318-28237592	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr6:28237252-28237674	MCF10A-Er-Src	breast:	n/a	chr6:28237482-28237493
40	POLR2A	chr6:28235400-28237811	K562	blood:	n/a	n/a
41	FOS	chr6:28237252-28237675	MCF10A-Er-Src	breast:	n/a	chr6:28237482-28237493
42	RCOR1	chr6:28237361-28237587	K562	blood:	n/a	n/a
43	YY1	chr6:28237338-28237702	SK-N-SH	brain:	n/a	n/a
44	CBX3	chr6:28237110-28237786	HCT-116	colon:	n/a	n/a
45	MAZ	chr6:28237372-28237445	K562	blood:	n/a	n/a
46	CTCF	chr6:28237340-28237490	HPAF	blood vessel:	n/a	n/a
47	TCF12	chr6:28237121-28237727	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr6:28237238-28237655	SK-N-SH	brain:	n/a	n/a
49	PBX3	chr6:28237178-28237700	SK-N-SH	brain:	n/a	n/a
50	MAFK	chr6:28237252-28237675	IMR90	lung:	n/a	chr6:28237483-28237498

No.	Distal block	Cell Line	Cell type
1	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
2	chr6:28235481..28237475-chr6:28323634..28325557,2	MCF-7	breast:
3	chr6:28234029..28236350-chr6:28236563..28238803,2	K562	blood:
4	chr6:28232169..28234255-chr6:28237329..28239836,2	MCF-7	breast:
5	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
6	chr6:28235909..28238714-chr6:28300665..28303049,3	MCF-7	breast:
7	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:
8	chr6:28234828..28238066-chr6:28314810..28319280,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197062	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10080420	0.80[ASN][1000 genomes]
rs10484404	1.00[JPT][hapmap]
rs1150700	0.92[YRI][hapmap]
rs1150715	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150722	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150723	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1150725	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332986	0.80[ASN][1000 genomes]
rs1600621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679723	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1736892	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1778510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108924	1.00[JPT][hapmap]
rs2191036	0.80[ASN][1000 genomes]
rs2799076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28475822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3757183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6456812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6456813	0.81[YRI][hapmap]
rs6456817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6456820	0.80[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6901001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6902583	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908459	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6910120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6918043	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6918631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6922161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927023	0.80[ASN][1000 genomes]
rs6929449	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6929559	1.00[JPT][hapmap]
rs6938371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6941222	0.80[ASN][1000 genomes]
rs7747772	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7752448	1.00[JPT][hapmap]
rs7752721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7759855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7767897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9295770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9461450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461452	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468328	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468337	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468341	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468375	0.86[ASN][1000 genomes]
rs9468384	0.80[ASN][1000 genomes]
rs9654587	0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235200-28239600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28235400-28239600	Weak transcription	Gastric	stomach
3	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
4	chr6:28235600-28238800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:28235600-28239200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:28235600-28239200	Weak transcription	Lung	lung
7	chr6:28235600-28239600	Weak transcription	Aorta	Aorta
8	chr6:28235600-28239600	Weak transcription	Esophagus	oesophagus
9	chr6:28235600-28239600	Weak transcription	Left Ventricle	heart
10	chr6:28235600-28239800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28235600-28239800	Weak transcription	Pancreas	Pancrea
12	chr6:28235600-28240000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:28235600-28243400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:28235800-28238200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:28235800-28239200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:28235800-28239200	Weak transcription	Right Ventricle	heart
19	chr6:28236000-28237800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:28236000-28237800	Enhancers	NHEK	skin
21	chr6:28236000-28238000	Enhancers	Hela-S3	cervix
22	chr6:28236000-28238800	Weak transcription	Fetal Stomach	stomach
23	chr6:28236000-28239200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:28236000-28239200	Weak transcription	Fetal Intestine Small	intestine
25	chr6:28236000-28239200	Weak transcription	Spleen	Spleen
26	chr6:28236000-28239400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:28236000-28239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:28236000-28239600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:28236000-28239600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr6:28236000-28239600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:28236000-28239600	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:28236000-28239600	Weak transcription	Placenta	Placenta
33	chr6:28236000-28239600	Weak transcription	Fetal Thymus	thymus
34	chr6:28236000-28239600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:28236000-28239600	Weak transcription	Thymus	Thymus
36	chr6:28236000-28239600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:28236000-28239800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:28236000-28239800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:28236000-28239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:28236200-28238800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:28236200-28239200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:28236200-28239200	Weak transcription	Brain Anterior Caudate	brain
43	chr6:28236200-28239400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:28236200-28239600	Weak transcription	Primary B cells from cord blood	blood
45	chr6:28236200-28239600	Weak transcription	Brain Substantia Nigra	brain
46	chr6:28236200-28239600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:28236200-28239600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:28236200-28239600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:28236200-28239800	Weak transcription	Liver	Liver
50	chr6:28236200-28239800	Weak transcription	Colonic Mucosa	Colon

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