Variant report

Variant	rs1407204
Chromosome Location	chr6:119289835-119289836
allele	A/C
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	CTCF	chr6:119289679-119289862	Pancreas_OC	pancreas:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
2	RAD21	chr6:119289594-119289955	A549	lung:	n/a	chr6:119289772-119289791
3	CTCF	chr6:119289508-119290133	HCT-116	colon:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
4	RAD21	chr6:119289535-119290041	MCF-7	breast:	n/a	chr6:119289772-119289791
5	CTCF	chr6:119289700-119289850	K562	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
6	CTCF	chr6:119289700-119289850	GM12868	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
7	RAD21	chr6:119289653-119289847	GM12878	blood:	n/a	chr6:119289772-119289791
8	RAD21	chr6:119289506-119290090	SK-N-SH	brain:	n/a	chr6:119289772-119289791
9	RAD21	chr6:119289532-119290071	HCT-116	colon:	n/a	chr6:119289772-119289791
10	RAD21	chr6:119289521-119289921	H1-hESC	embryonic stem cell:	n/a	chr6:119289772-119289791
11	RAD21	chr6:119289620-119289910	SK-N-SH_RA	brain:	n/a	chr6:119289772-119289791
12	CTCF	chr6:119289720-119289870	HRE	kidney:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
13	CTCF	chr6:119289740-119289890	HEEpiC	esophagus:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
14	RAD21	chr6:119289563-119289993	HepG2	liver:	n/a	chr6:119289772-119289791
15	CTCF	chr6:119289720-119289870	HMEC	breast:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
16	CTCF	chr6:119289700-119289850	AG04450	lung:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
17	CTCF	chr6:119289820-119289970	NHDF-neo	bronchial:	n/a	n/a
18	CTCF	chr6:119289700-119289850	SAEC	small airway:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
19	CTCF	chr6:119289689-119289847	GM10266	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
20	RAD21	chr6:119289586-119289913	SK-N-SH_RA	brain:	n/a	chr6:119289772-119289791
21	RAD21	chr6:119289589-119290026	A549	lung:	n/a	chr6:119289772-119289791
22	CTCF	chr6:119289688-119289852	LNCaP	prostate:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
23	CTCF	chr6:119289693-119289844	Lung_OC	lung:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
24	CTCF	chr6:119289582-119289898	MCF-7	breast:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
25	CTCF	chr6:119289663-119289888	K562	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
26	SMC3	chr6:119289418-119290445	SK-N-SH	brain:	n/a	chr6:119289773-119289787
27	CTCF	chr6:119289760-119289910	BJ	skin:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
28	CTCF	chr6:119289700-119289850	GM12864	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
29	CTCF	chr6:119289655-119289883	HepG2	liver:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
30	CTCF	chr6:119289663-119289859	GM12878	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
31	CTCF	chr6:119289780-119289930	MCF-7	breast:	n/a	n/a
32	CTCF	chr6:119289720-119289870	HL-60	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
33	SMC3	chr6:119289652-119289951	K562	blood:	n/a	chr6:119289773-119289787
34	CTCF	chr6:119289700-119289850	GM12872	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
35	CTCF	chr6:119289740-119289890	RPTEC	kidney:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
36	CTCF	chr6:119289633-119289953	GM12878	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
37	CTCF	chr6:119289664-119289909	IMR90	lung:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
38	CTCF	chr6:119289700-119289850	HPAF	blood vessel:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
39	CTCF	chr6:119289668-119289884	SK-N-SH_RA	brain:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
40	RAD21	chr6:119289590-119289996	H1-hESC	embryonic stem cell:	n/a	chr6:119289772-119289791
41	RAD21	chr6:119289578-119289914	ECC-1	luminal epithelium:	n/a	chr6:119289772-119289791
42	CTCF	chr6:119289694-119289857	MCF-7	breast:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
43	CTCF	chr6:119289720-119289870	AG04450	lung:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
44	CTCF	chr6:119289714-119289837	HepG2	liver:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
45	CTCF	chr6:119289626-119289914	Medullo	brain:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
46	SMC3	chr6:119289697-119289895	GM12878	blood:	n/a	chr6:119289773-119289787
47	CTCF	chr6:119289740-119289890	BE2_C	brain:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
48	ZNF143	chr6:119289692-119289926	K562	blood:	n/a	n/a
49	CTCF	chr6:119289760-119289910	GM12864	blood:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794
50	CTCF	chr6:119289501-119290137	A549	lung:	n/a	chr6:119289771-119289789 chr6:119289772-119289788 chr6:119289773-119289794

No.	Distal block	Cell Line	Cell type
1	chr6:119289690..119290275-chr6:119431681..119432394,3	MCF-7	breast:
2	chr6:119289252..119290236-chr6:119431679..119432411,3	MCF-7	breast:
3	chr6:119287930..119290398-chr6:119293671..119295225,2	K562	blood:
4	chr6:119289475..119290061-chr6:119399611..119400273,2	MCF-7	breast:
5	chr6:119289080..119290784-chr6:119295279..119297074,2	K562	blood:
6	chr6:119289303..119290241-chr6:119431643..119432582,8	K562	blood:

Variant related genes	Relation type
FAM184A	TF binding region
ENSG00000111879	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1087451	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1087452	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12529321	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13209700	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13214708	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1321837	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13219598	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17827619	0.83[ASN][1000 genomes]
rs2145568	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs284921	1.00[CHB][hapmap]
rs34455711	0.89[ASN][1000 genomes]
rs35375291	0.84[EUR][1000 genomes]
rs35795136	0.89[ASN][1000 genomes]
rs3822955	0.89[ASN][1000 genomes]
rs4245501	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4946368	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61108921	0.97[ASN][1000 genomes]
rs65685	1.00[CHB][hapmap]
rs6915609	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6915914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6929592	1.00[JPT][hapmap]
rs6934262	0.82[JPT][hapmap]
rs706972	1.00[CHB][hapmap]
rs71559845	0.89[ASN][1000 genomes]
rs7743694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746114	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7766260	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs794602	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs794609	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs794610	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs794612	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs794613	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs794615	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs927288	0.89[ASN][1000 genomes]
rs9372516	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9374758	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9385064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9401108	0.93[CEU][hapmap];1.00[CHB][hapmap]

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119279600-119298200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:119279800-119303600	Weak transcription	Adipose Nuclei	Adipose
3	chr6:119280000-119305200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:119280400-119293000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:119281400-119293200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:119281600-119298000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:119281600-119298000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:119281600-119299400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:119281600-119303200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:119283600-119302400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:119285200-119304400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:119285800-119340000	Weak transcription	Fetal Brain Male	brain
13	chr6:119286000-119293000	Weak transcription	Lung	lung
14	chr6:119286000-119300000	Weak transcription	Brain Anterior Caudate	brain
15	chr6:119286000-119302800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:119286800-119298200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:119287200-119299400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:119287200-119305000	Weak transcription	HepG2	liver
19	chr6:119287200-119326600	Weak transcription	Fetal Brain Female	brain
20	chr6:119287400-119330000	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:119287600-119300200	Weak transcription	Placenta	Placenta
22	chr6:119287800-119296200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:119288400-119292800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:119288800-119299000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:119288800-119315000	Weak transcription	Fetal Intestine Large	intestine
26	chr6:119289200-119304600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links