Variant report

Variant	rs3777556
Chromosome Location	chr6:45890641-45890642
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	chr6:45890640-45890790	GM12866	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
2	CTCF	chr6:45890599-45890804	GM13976	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
3	RAD21	chr6:45890447-45891003	A549	lung:	n/a	chr6:45890696-45890715
4	RAD21	chr6:45890383-45890805	H1-hESC	embryonic stem cell:	n/a	chr6:45890696-45890715
5	CTCF	chr6:45890579-45890792	MCF-7	breast:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
6	CTCF	chr6:45890620-45890770	AG04449	skin:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
7	MAZ	chr6:45890526-45890938	GM12878	blood:	n/a	n/a
8	RAD21	chr6:45890409-45890836	SK-N-SH_RA	brain:	n/a	chr6:45890696-45890715
9	RAD21	chr6:45890567-45890802	HepG2	liver:	n/a	chr6:45890696-45890715
10	EBF1	chr6:45890573-45890807	GM12878	blood:	n/a	n/a
11	MYC	chr6:45890620-45890762	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr6:45890640-45890790	Caco-2	colon:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
13	CTCF	chr6:45890580-45890730	HUVEC	blood vessel:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
14	CTCF	chr6:45890620-45890770	GM12865	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
15	CTCF	chr6:45890479-45890779	T-47D	breast:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
16	RAD21	chr6:45890206-45890980	Hela-S3	cervix:	n/a	chr6:45890696-45890715
17	TBL1XR1	chr6:45890580-45890795	K562	blood:	n/a	n/a
18	CTCF	chr6:45890640-45890790	AG10803	skin:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
19	IRF3	chr6:45890585-45890933	GM12878	blood:	n/a	n/a
20	SMC3	chr6:45890536-45890878	HepG2	liver:	n/a	chr6:45890700-45890714
21	CTCF	chr6:45890640-45890790	MCF-7	breast:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
22	CTCF	chr6:45890581-45890819	K562	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
23	STAT3	chr6:45890604-45890723	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr6:45890640-45890790	GM12873	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
25	CTCF	chr6:45890547-45890791	Fibrobl	skin:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
26	CTCF	chr6:45890397-45891044	HCT-116	colon:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
27	CTCF	chr6:45890640-45890790	BJ	skin:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
28	STAT5A	chr6:45890494-45890911	GM12878	blood:	n/a	n/a
29	MYC	chr6:45890576-45890764	MCF10A-Er-Src	breast:	n/a	n/a
30	CTCF	chr6:45890620-45890770	AG10803	skin:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
31	CTCF	chr6:45890600-45890750	Hela-S3	cervix:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
32	CTCF	chr6:45890600-45890750	BE2_C	brain:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
33	CTCF	chr6:45890574-45890822	Pancreas_OC	pancreas:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
34	CTCF	chr6:45890592-45890801	MCF-7	breast:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
35	TCF7L2	chr6:45890485-45890801	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr6:45890600-45890750	GM12872	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
37	CTCF	chr6:45890600-45890750	SAEC	small airway:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
38	CTCF	chr6:45890600-45890750	NHEK	skin:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
39	CTCF	chr6:45890557-45890828	MCF-7	breast:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
40	CTCF	chr6:45890620-45890770	GM12874	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
41	CTCF	chr6:45890559-45890828	HepG2	liver:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
42	CTCF	chr6:45890620-45890770	HVMF	connective:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
43	RAD21	chr6:45890436-45890874	ECC-1	luminal epithelium:	n/a	chr6:45890696-45890715
44	RAD21	chr6:45890465-45891017	GM12878	blood:	n/a	chr6:45890696-45890715
45	STAT1	chr6:45890600-45890805	GM12878	blood:	n/a	n/a
46	CTCF	chr6:45890570-45890799	GM12892	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
47	CTCF	chr6:45890570-45890843	Spleen_OC	spleen:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
48	CTCF	chr6:45890574-45890798	A549	lung:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
49	CTCF	chr6:45890613-45890839	GM20000	blood:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714
50	JUND	chr6:45890404-45890869	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:45623457..45625814-chr6:45890186..45892755,2	MCF-7	breast:
2	chr6:45756761..45757645-chr6:45890500..45891157,2	MCF-7	breast:
3	chr6:44560942..44561805-chr6:45890244..45890927,2	MCF-7	breast:
4	chr6:44623182..44623933-chr6:45889938..45891174,4	K562	blood:
5	chr6:44443149..44444048-chr6:45890206..45890910,3	K562	blood:

Variant related genes	Relation type
CLIC5	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10807328	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12204991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665031	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1361215	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1416166	0.80[CHD][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes]
rs1416167	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2105168	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2894657	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3729618	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777544	0.80[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs3777546	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777547	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777548	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777552	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777553	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798259	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822876	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822878	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822879	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822880	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822881	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714890	1.00[CEU][hapmap];0.82[TSI][hapmap];0.93[EUR][1000 genomes]
rs58427559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6939554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9367228	0.81[GIH][hapmap]
rs9367229	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369590	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395135	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1021917	chr6:45879064-45898314	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45866600-45898400	Weak transcription	Colonic Mucosa	Colon
2	chr6:45881200-45908000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:45882200-45890800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:45882200-45891200	Weak transcription	Placenta	Placenta
5	chr6:45882400-45898400	Weak transcription	Fetal Intestine Large	intestine
6	chr6:45885200-45891200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:45886800-45892000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
9	chr6:45887000-45892000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:45887400-45896600	Weak transcription	Fetal Intestine Small	intestine
11	chr6:45887800-45892800	Enhancers	GM12878-XiMat	blood
12	chr6:45888400-45892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:45888400-45892800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:45888600-45892400	Enhancers	HSMM	muscle
15	chr6:45889000-45891400	Weak transcription	NH-A	brain
16	chr6:45889000-45891800	Enhancers	Right Ventricle	heart
17	chr6:45889200-45891400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:45889200-45897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:45889400-45891000	Enhancers	Fetal Lung	lung
20	chr6:45889400-45891400	Enhancers	Fetal Heart	heart
21	chr6:45889400-45892200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:45889400-45892200	Enhancers	NHDF-Ad	bronchial
23	chr6:45889400-45892400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:45889400-45892400	Enhancers	HSMMtube	muscle
25	chr6:45889600-45890800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:45889600-45891000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:45889600-45891000	Enhancers	Adipose Nuclei	Adipose
28	chr6:45889600-45891200	Enhancers	Hela-S3	cervix
29	chr6:45889600-45891800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:45889600-45891800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:45889600-45891800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:45889600-45892200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:45889800-45890800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:45889800-45891000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:45890000-45891600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:45890000-45898000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:45890000-45898000	Weak transcription	Right Atrium	heart
38	chr6:45890000-45898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:45890400-45890800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:45890400-45890800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
41	chr6:45890400-45890800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:45890400-45891000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:45890400-45891000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:45890400-45891000	Enhancers	Fetal Kidney	kidney
45	chr6:45890400-45891600	Weak transcription	Fetal Stomach	stomach
46	chr6:45890400-45892200	Enhancers	Osteobl	bone
47	chr6:45890400-45892400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:45890400-45892800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:45890600-45890800	Enhancers	Primary B cells from peripheral blood	blood
50	chr6:45890600-45891600	Enhancers	Left Ventricle	heart

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