Variant report

Variant	rs3778418
Chromosome Location	chr6:166928704-166928705
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	CTCF	chr6:166928640-166928790	BJ	skin:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
2	STAT3	chr6:166928672-166928872	MCF10A-Er-Src	breast:	n/a	chr6:166928762-166928771 chr6:166928761-166928770
3	JUND	chr6:166928594-166928916	K562	blood:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928762-166928770
4	RAD21	chr6:166928492-166928895	SK-N-SH_RA	brain:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
5	CTCF	chr6:166928656-166928811	GM12891	blood:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
6	JUN	chr6:166928489-166929142	K562	blood:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928791-166928804 chr6:166928762-166928770
7	RAD21	chr6:166928370-166929127	HCT-116	colon:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
8	CTCF	chr6:166928640-166928790	WERI-Rb-1	eye:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
9	CTCF	chr6:166928620-166928770	HAc	cerebellar:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
10	FOS	chr6:166928576-166928994	MCF10A-Er-Src	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928760-166928771 chr6:166928762-166928770
11	CTCF	chr6:166928606-166928855	MCF-7	breast:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
12	CTCF	chr6:166928600-166928750	SK-N-SH_RA	brain:	n/a	chr6:166928722-166928731
13	FOSL1	chr6:166928365-166929187	HCT-116	colon:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
14	CTCF	chr6:166928680-166928830	HMF	breast:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
15	CTCF	chr6:166928641-166928791	SK-N-SH_RA	brain:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
16	FOSL1	chr6:166928422-166929142	HCT-116	colon:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
17	CTCF	chr6:166928650-166928812	A549	lung:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
18	CTCF	chr6:166928518-166928837	MCF-7	breast:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
19	JUN	chr6:166928688-166928856	K562	blood:	n/a	chr6:166928762-166928769 chr6:166928791-166928804 chr6:166928762-166928770
20	E2F4	chr6:166928682-166928810	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr6:166928568-166929065	U87	brain:	n/a	n/a
22	CTCF	chr6:166928700-166928850	AG09309	skin:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
23	CTCF	chr6:166928587-166928844	Gliobla	brain:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
24	CTCF	chr6:166928680-166928830	HA-sp	spinal cord:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
25	SMC3	chr6:166927598-166929040	SK-N-SH	brain:	n/a	chr6:166927823-166927837 chr6:166927823-166927830
26	RAD21	chr6:166928508-166928872	MCF-7	breast:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
27	CTCF	chr6:166928660-166928810	GM12878	blood:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
28	RAD21	chr6:166928669-166928803	Hela-S3	cervix:	n/a	chr6:166928721-166928730 chr6:166928741-166928754
29	STAT3	chr6:166928672-166928880	MCF10A-Er-Src	breast:	n/a	chr6:166928762-166928771 chr6:166928761-166928770
30	FOS	chr6:166928575-166928969	MCF10A-Er-Src	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928760-166928771 chr6:166928762-166928770
31	CTCF	chr6:166928680-166928830	GM12865	blood:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
32	CTCF	chr6:166928640-166928790	NHEK	skin:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
33	JUND	chr6:166928683-166928806	H1-hESC	embryonic stem cell:	n/a	chr6:166928762-166928769 chr6:166928762-166928770
34	CTCF	chr6:166928620-166928770	HFF	foreskin:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
35	CTCF	chr6:166928640-166928790	NB4	blood:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
36	CEBPB	chr6:166928607-166929177	IMR90	lung:	n/a	n/a
37	CTCF	chr6:166928599-166928855	NHEK	skin:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
38	CTCF	chr6:166928620-166928770	HPF	lung:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
39	CTCF	chr6:166928619-166928850	MCF-7	breast:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
40	CTCF	chr6:166928640-166928790	NHLF	lung:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
41	CTCF	chr6:166928580-166928730	HFF-Myc	foreskin:	n/a	n/a
42	JUND	chr6:166928689-166928811	H1-hESC	embryonic stem cell:	n/a	chr6:166928762-166928769 chr6:166928762-166928770
43	CEBPB	chr6:166928642-166928852	Hela-S3	cervix:	n/a	n/a
44	FOSL2	chr6:166928567-166928876	HepG2	liver:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928762-166928770
45	CTCF	chr6:166928617-166928819	MCF-7	breast:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
46	RCOR1	chr6:166927751-166929314	IMR90	lung:	n/a	n/a
47	CTCF	chr6:166928680-166928830	HBMEC	blood vessel:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
48	TCF12	chr6:166928402-166929170	SK-N-SH	brain:	n/a	n/a
49	CTCF	chr6:166928640-166928790	HMF	breast:	n/a	chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
50	CTCF	chr6:166928600-166928750	GM06990	blood:	n/a	chr6:166928722-166928731

No.	Distal block	Cell Line	Cell type
1	chr6:166928469..166930058-chr6:167040238..167042581,2	MCF-7	breast:
2	chr6:166869518..166870276-chr6:166927954..166928779,2	MCF-7	breast:
3	chr6:166928192..166929030-chr6:167027760..167028686,4	MCF-7	breast:

Variant related genes	Relation type
RPS6KA2	TF binding region
ENSG00000071242	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10214537	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs12528147	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12528167	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs35302651	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3757193	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3778409	1.00[YRI][hapmap]
rs3778412	0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs3778422	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799632	0.81[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs3799647	0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs3799654	0.90[EUR][1000 genomes]
rs3799658	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3799667	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799670	0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs55665778	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7765185	1.00[CEU][hapmap]
rs9364856	1.00[YRI][hapmap]
rs9457174	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	esv1806956	chr6:166928580-166938431	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166899400-166929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:166909600-166943800	Weak transcription	Colonic Mucosa	Colon
6	chr6:166912200-166931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:166913000-166929000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:166913000-166952000	Weak transcription	Primary T cells from cord blood	blood
9	chr6:166916200-166954200	Weak transcription	Right Atrium	heart
10	chr6:166916400-166940400	Weak transcription	Fetal Heart	heart
11	chr6:166917200-166932000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:166918400-166931400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:166921200-166930000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:166921400-166930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:166921400-166930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:166921400-166943600	Weak transcription	Fetal Lung	lung
17	chr6:166921600-166932000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:166921600-166932000	Weak transcription	Fetal Kidney	kidney
19	chr6:166921600-166937400	Weak transcription	Fetal Brain Male	brain
20	chr6:166922400-166929400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:166923000-166930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:166923000-166930000	Weak transcription	Esophagus	oesophagus
23	chr6:166923000-166931400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:166923000-166937200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:166923000-166940400	Weak transcription	Aorta	Aorta
26	chr6:166923000-166943800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:166923200-166931200	Weak transcription	Brain Germinal Matrix	brain
28	chr6:166923200-166932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:166923200-166940200	Weak transcription	Ovary	ovary
30	chr6:166923200-166943200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:166923200-166943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:166923600-166936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:166923800-166930000	Weak transcription	Placenta	Placenta
34	chr6:166923800-166944400	Weak transcription	Psoas Muscle	Psoas
35	chr6:166923800-166953000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:166924600-166928800	Weak transcription	HSMMtube	muscle
37	chr6:166925000-166940400	Weak transcription	Adipose Nuclei	Adipose
38	chr6:166926200-166929000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr6:166926200-166930400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:166926200-166930400	Strong transcription	Fetal Stomach	stomach
41	chr6:166926400-166929200	Strong transcription	Fetal Muscle Leg	muscle
42	chr6:166926600-166928800	Strong transcription	Pancreas	Pancrea
43	chr6:166926600-166928800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:166927000-166929000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:166927000-166930400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:166927200-166938000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:166927400-166928800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:166927600-166928800	Strong transcription	Gastric	stomach
49	chr6:166927600-166929400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:166927600-166929600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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