Variant report

Variant	rs3777559
Chromosome Location	chr6:45892154-45892155
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	BCL11A	chr6:45891715-45892190	GM12878	blood:	n/a	n/a
2	NFATC1	chr6:45891702-45892247	GM12878	blood:	n/a	n/a
3	PAX5	chr6:45891643-45892274	GM12878	blood:	n/a	n/a
4	IKZF1	chr6:45891658-45892283	GM12878	blood:	n/a	n/a
5	NFATC1	chr6:45891687-45892207	GM12878	blood:	n/a	n/a
6	ATF2	chr6:45891623-45892285	GM12878	blood:	n/a	n/a
7	FOXM1	chr6:45891572-45892338	GM12878	blood:	n/a	n/a
8	STAT5A	chr6:45891705-45892291	GM12878	blood:	n/a	n/a
9	CREB1	chr6:45891531-45892217	GM12878	blood:	n/a	n/a
10	CEBPB	chr6:45891678-45892205	GM12878	blood:	n/a	n/a
11	PML	chr6:45891677-45892255	GM12878	blood:	n/a	chr6:45891914-45891923
12	TCF3	chr6:45891696-45892229	GM12878	blood:	n/a	n/a
13	RELA	chr6:45891816-45892220	GM12878	blood:	n/a	n/a
14	MTA3	chr6:45891606-45892277	GM12878	blood:	n/a	n/a
15	CREB1	chr6:45891638-45892231	GM12878	blood:	n/a	n/a
16	RUNX3	chr6:45891609-45892209	GM12878	blood:	n/a	n/a
17	STAT5A	chr6:45891600-45892161	GM12878	blood:	n/a	n/a
18	EBF1	chr6:45891884-45892165	GM12878	blood:	n/a	n/a
19	FOXM1	chr6:45891665-45892299	GM12878	blood:	n/a	n/a
20	TCF12	chr6:45891797-45892159	GM12878	blood:	n/a	chr6:45892102-45892109 chr6:45891897-45891906
21	MTA3	chr6:45891768-45892197	GM12878	blood:	n/a	n/a
22	BATF	chr6:45891559-45892218	GM12878	blood:	n/a	chr6:45891913-45891924
23	RUNX3	chr6:45891674-45892198	GM12878	blood:	n/a	n/a
24	MEF2A	chr6:45891700-45892207	GM12878	blood:	n/a	n/a
25	EP300	chr6:45891711-45892214	GM12878	blood:	n/a	chr6:45891896-45891906
26	POLR2A	chr6:45891623-45892285	GM12892	blood:	n/a	n/a
27	IRF4	chr6:45891665-45892203	GM12878	blood:	n/a	n/a
28	NFIC	chr6:45891545-45892306	GM12878	blood:	n/a	n/a
29	RELA	chr6:45891727-45892219	GM19193	blood:	n/a	n/a
30	BCL3	chr6:45891683-45892212	GM12878	blood:	n/a	n/a
31	BATF	chr6:45891765-45892170	GM12878	blood:	n/a	chr6:45891913-45891924
32	POU2F2	chr6:45891765-45892260	GM12891	blood:	n/a	n/a
33	TCF12	chr6:45891785-45892181	GM12878	blood:	n/a	chr6:45892102-45892109 chr6:45891897-45891906
34	MEF2C	chr6:45891688-45892219	GM12878	blood:	n/a	n/a
35	ATF2	chr6:45891752-45892199	GM12878	blood:	n/a	n/a
36	TCF3	chr6:45891758-45892172	GM12878	blood:	n/a	n/a
37	NFIC	chr6:45891590-45892361	GM12878	blood:	n/a	n/a
38	BCLAF1	chr6:45891671-45892218	GM12878	blood:	n/a	n/a
39	EBF1	chr6:45891597-45892191	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45623457..45625814-chr6:45890186..45892755,2	MCF-7	breast:
2	chr6:44620218..44622571-chr6:45890865..45893250,2	MCF-7	breast:

Variant related genes	Relation type
CLIC5	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10807328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665031	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1361215	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1416166	0.85[AMR][1000 genomes]
rs1416167	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105168	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894657	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3729618	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777544	0.94[ASN][1000 genomes]
rs3777546	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777547	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777548	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777554	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777561	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798258	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822876	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822878	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822879	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822880	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822881	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714890	0.93[EUR][1000 genomes]
rs58427559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904888	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6939554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367229	0.99[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369590	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9381410	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395135	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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:40 , 50 per page) page: 1

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	chr6:45882400-45898400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
5	chr6:45887400-45896600	Weak transcription	Fetal Intestine Small	intestine
6	chr6:45887800-45892800	Enhancers	GM12878-XiMat	blood
7	chr6:45888400-45892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:45888400-45892800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:45888600-45892400	Enhancers	HSMM	muscle
10	chr6:45889200-45897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:45889400-45892200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr6:45889400-45892200	Enhancers	NHDF-Ad	bronchial
13	chr6:45889400-45892400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:45889400-45892400	Enhancers	HSMMtube	muscle
15	chr6:45889600-45892200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:45890000-45898000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:45890000-45898000	Weak transcription	Right Atrium	heart
18	chr6:45890000-45898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:45890400-45892200	Enhancers	Osteobl	bone
20	chr6:45890400-45892400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:45890400-45892800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:45890600-45894800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:45890600-45901600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:45890800-45892200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:45891000-45898400	Weak transcription	Fetal Kidney	kidney
26	chr6:45891200-45892800	Enhancers	Placenta	Placenta
27	chr6:45891400-45892200	Enhancers	NH-A	brain
28	chr6:45891400-45898000	Weak transcription	Fetal Heart	heart
29	chr6:45891600-45892200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr6:45891600-45892200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:45891600-45892200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:45891600-45892200	Enhancers	Fetal Stomach	stomach
33	chr6:45891600-45892200	Enhancers	NHEK	skin
34	chr6:45891600-45898400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:45891800-45896400	Weak transcription	Right Ventricle	heart
36	chr6:45891800-45896600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:45892000-45892200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:45892000-45892600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:45892000-45893200	Weak transcription	Left Ventricle	heart
40	chr6:45892000-45895600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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