Variant report

Variant	rs1233712
Chromosome Location	chr6:28193131-28193132
allele	A/G
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	ELF1	chr6:28192523-28193531	HCT-116	colon:	n/a	chr6:28193008-28193017 chr6:28193007-28193018
2	POLR2A	chr6:28192765-28193340	HL-60	blood:	n/a	n/a
3	GABPA	chr6:28192847-28193226	GM12878	blood:	n/a	n/a
4	KAP1	chr6:28192909-28193371	HEK293	kidney:	n/a	n/a
5	MYC	chr6:28192946-28193139	MCF-7	breast:	n/a	n/a
6	MAX	chr6:28192836-28193303	K562	blood:	n/a	chr6:28193246-28193256
7	POLR2A	chr6:28192699-28193537	H1-neurons	neurons:	n/a	n/a
8	TAF1	chr6:28192775-28193391	H1-neurons	neurons:	n/a	n/a
9	TCF3	chr6:28192816-28193249	GM12878	blood:	n/a	n/a
10	RCOR1	chr6:28192895-28193227	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:28192810-28193448	GM12878	blood:	n/a	n/a
12	SIX5	chr6:28192625-28193357	A549	lung:	n/a	n/a
13	POLR2A	chr6:28192796-28193390	H1-hESC	embryonic stem cell:	n/a	n/a
14	ELF1	chr6:28192775-28193335	HepG2	liver:	n/a	chr6:28193008-28193017 chr6:28193007-28193018
15	ETS1	chr6:28192883-28193325	K562	blood:	n/a	chr6:28193010-28193020 chr6:28193009-28193018 chr6:28193009-28193018 chr6:28193009-28193020 chr6:28193249-28193260
16	GABPA	chr6:28192781-28193310	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFIC	chr6:28192720-28193492	HepG2	liver:	n/a	n/a
18	ELF1	chr6:28192590-28193539	HCT-116	colon:	n/a	chr6:28193008-28193017 chr6:28193007-28193018
19	ZKSCAN1	chr6:28192823-28193209	Hela-S3	cervix:	n/a	n/a
20	REST	chr6:28192826-28193265	SK-N-SH	brain:	n/a	n/a
21	ZNF263	chr6:28192862-28193577	HEK293-T-REx	kidney:	n/a	n/a
22	ETS1	chr6:28192819-28193206	A549	lung:	n/a	chr6:28193010-28193020 chr6:28193009-28193018 chr6:28193009-28193018 chr6:28193009-28193020
23	SP2	chr6:28192668-28193414	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr6:28192769-28193505	H1-neurons	neurons:	n/a	n/a
25	MYC	chr6:28192953-28193199	MCF-7	breast:	n/a	n/a
26	POLR2A	chr6:28192723-28193497	GM18951	blood:	n/a	n/a
27	POLR2A	chr6:28192501-28193454	GM12878	blood:	n/a	n/a
28	BHLHE40	chr6:28192949-28193276	A549	lung:	n/a	n/a
29	FOSL2	chr6:28192660-28193273	A549	lung:	n/a	n/a
30	ZNF143	chr6:28192827-28193336	K562	blood:	n/a	n/a
31	MAX	chr6:28192679-28193409	SK-N-SH	brain:	n/a	chr6:28193246-28193256
32	SIX5	chr6:28192888-28193167	A549	lung:	n/a	n/a
33	MAX	chr6:28192797-28193405	ECC-1	luminal epithelium:	n/a	chr6:28193246-28193256
34	STAT3	chr6:28192743-28193148	MCF10A-Er-Src	breast:	n/a	n/a
35	RELA	chr6:28192534-28193201	GM19099	blood:	n/a	n/a
36	POLR2A	chr6:28192738-28193398	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:28192710-28193378	HCT-116	colon:	n/a	n/a
38	ELF1	chr6:28192692-28193426	MCF-7	breast:	n/a	chr6:28193008-28193017 chr6:28193007-28193018
39	SP2	chr6:28192677-28193401	HepG2	liver:	n/a	n/a
40	MXI1	chr6:28192892-28193296	H1-hESC	embryonic stem cell:	n/a	n/a
41	EP300	chr6:28192465-28193234	K562	blood:	n/a	chr6:28193010-28193017 chr6:28192699-28192712
42	ELF1	chr6:28192789-28193230	HepG2	liver:	n/a	chr6:28193008-28193017 chr6:28193007-28193018
43	YY1	chr6:28192758-28193372	GM12878	blood:	n/a	chr6:28193251-28193260
44	CBX3	chr6:28192760-28193259	K562	blood:	n/a	n/a
45	EGR1	chr6:28192786-28193421	K562	blood:	n/a	chr6:28193248-28193258 chr6:28193246-28193259 chr6:28193249-28193259 chr6:28193246-28193259 chr6:28193009-28193018 chr6:28193245-28193260
46	MAX	chr6:28192802-28193442	MCF-7	breast:	n/a	chr6:28193246-28193256
47	FOXA1	chr6:28192926-28193137	T-47D	breast:	n/a	n/a
48	REST	chr6:28192784-28193195	PANC-1	pancreas:	n/a	n/a
49	ELK4	chr6:28192629-28193270	Hela-S3	cervix:	n/a	chr6:28193008-28193019
50	YY1	chr6:28192927-28193214	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28184931..28189194-chr6:28190077..28194573,12	MCF-7	breast:
2	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
3	chr17:8076441..8077151-chr6:28192729..28193485,2	Hela-S3	cervix:
4	chr6:28191649..28195458-chr6:28301378..28307708,9	K562	blood:
5	chr6:28129397..28131360-chr6:28191862..28193480,2	K562	blood:
6	chr6:28191774..28193950-chr6:28248058..28250874,2	K562	blood:
7	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
8	chr6:28103649..28105487-chr6:28192545..28194839,2	MCF-7	breast:
9	chr6:28102806..28106129-chr6:28190797..28194598,4	K562	blood:
10	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
11	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
12	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
13	chr6:28191934..28194357-chr6:28233804..28235938,2	MCF-7	breast:
14	chr6:28191542..28194803-chr6:28365970..28368645,4	K562	blood:
15	chr6:27859047..27860986-chr6:28192686..28194393,2	K562	blood:
16	chr6:28192051..28194433-chr6:28219534..28221191,2	MCF-7	breast:
17	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
18	chr6:28108436..28110620-chr6:28192837..28194996,3	MCF-7	breast:
19	chr6:28108043..28113786-chr6:28190485..28194607,10	K562	blood:
20	chr6:28191542..28193155-chr6:28365970..28368318,2	K562	blood:
21	chr6:27798954..27801175-chr6:28191953..28194580,2	K562	blood:
22	chr6:27857150..27860070-chr6:28191777..28193436,2	K562	blood:

Variant related genes	Relation type
ZSCAN9	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1150701	0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150702	0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150708	0.91[AFR][1000 genomes]
rs1150712	0.83[AMR][1000 genomes]
rs1736893	0.89[JPT][hapmap]
rs1778469	0.89[JPT][hapmap]
rs988083	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs988084	0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28192400-28193400	Active TSS	Liver	Liver
2	chr6:28192400-28193600	Active TSS	Primary B cells from cord blood	blood
3	chr6:28192400-28193600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr6:28192400-28193600	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr6:28192400-28193800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:28192400-28194000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:28192400-28194000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:28192400-28194000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:28192400-28194000	Active TSS	Fetal Kidney	kidney
10	chr6:28192400-28194000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:28192400-28194000	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:28192400-28194000	Active TSS	Right Ventricle	heart
13	chr6:28192400-28194000	Active TSS	HSMM	muscle
14	chr6:28192400-28194200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:28192400-28194200	Active TSS	Psoas Muscle	Psoas
16	chr6:28192400-28194200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr6:28192400-28194400	Active TSS	NHLF	lung
18	chr6:28192600-28193200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr6:28192600-28193200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:28192600-28193400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:28192600-28193400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:28192600-28193400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:28192600-28193400	Active TSS	Colon Smooth Muscle	Colon
24	chr6:28192600-28193400	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:28192600-28193600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:28192600-28193600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:28192600-28193600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:28192600-28193600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
29	chr6:28192600-28193600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
30	chr6:28192600-28193600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:28192600-28193600	Active TSS	Aorta	Aorta
32	chr6:28192600-28193600	Active TSS	Brain Angular Gyrus	brain
33	chr6:28192600-28193600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:28192600-28193600	Active TSS	Brain Substantia Nigra	brain
35	chr6:28192600-28193600	Active TSS	Colonic Mucosa	Colon
36	chr6:28192600-28193600	Active TSS	Fetal Brain Male	brain
37	chr6:28192600-28193600	Active TSS	Left Ventricle	heart
38	chr6:28192600-28193600	Active TSS	Ovary	ovary
39	chr6:28192600-28193600	Active TSS	Stomach Mucosa	stomach
40	chr6:28192600-28193800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:28192600-28193800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
42	chr6:28192600-28193800	Active TSS	Fetal Heart	heart
43	chr6:28192600-28193800	Active TSS	Lung	lung
44	chr6:28192600-28193800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr6:28192600-28193800	Bivalent/Poised TSS	HepG2	liver
46	chr6:28192600-28193800	Active TSS	NHDF-Ad	bronchial
47	chr6:28192600-28194000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:28192600-28194000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:28192600-28194000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:28192600-28194000	Active TSS	Fetal Intestine Large	intestine

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