Variant report

Variant	rs3777558
Chromosome Location	chr6:45891299-45891300
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	RFX5	chr6:45891055-45892016	IMR90	lung:	n/a	n/a
2	RUNX3	chr6:45890929-45891333	GM12878	blood:	n/a	n/a
3	CTCF	chr6:45890080-45891432	SK-N-SH	brain:	n/a	chr6:45890699-45890715 chr6:45890698-45890716 chr6:45890693-45890714

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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665031	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1361215	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1416166	0.85[AMR][1000 genomes]
rs1416167	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105168	0.90[AFR][1000 genomes];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	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777544	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3777546	0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777547	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777548	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777552	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777553	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777554	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777556	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]
rs3777557	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];1.00[ASN][1000 genomes]
rs3777561	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798258	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798259	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822876	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822878	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822879	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822880	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822881	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714890	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs58427559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904888	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6939554	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349335	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367229	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369590	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9381410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395135	1.00[AFR][1000 genomes];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:41 , 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	chr6:45886800-45892000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
6	chr6:45887000-45892000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:45887400-45896600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:45887800-45892800	Enhancers	GM12878-XiMat	blood
9	chr6:45888400-45892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:45888400-45892800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:45888600-45892400	Enhancers	HSMM	muscle
12	chr6:45889000-45891400	Weak transcription	NH-A	brain
13	chr6:45889000-45891800	Enhancers	Right Ventricle	heart
14	chr6:45889200-45891400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:45889200-45897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:45889400-45891400	Enhancers	Fetal Heart	heart
17	chr6:45889400-45892200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:45889400-45892200	Enhancers	NHDF-Ad	bronchial
19	chr6:45889400-45892400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:45889400-45892400	Enhancers	HSMMtube	muscle
21	chr6:45889600-45891800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:45889600-45891800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:45889600-45891800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:45889600-45892200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:45890000-45891600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:45890000-45898000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:45890000-45898000	Weak transcription	Right Atrium	heart
28	chr6:45890000-45898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:45890400-45891600	Weak transcription	Fetal Stomach	stomach
30	chr6:45890400-45892200	Enhancers	Osteobl	bone
31	chr6:45890400-45892400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:45890400-45892800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:45890600-45891600	Enhancers	Left Ventricle	heart
34	chr6:45890600-45894800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:45890600-45901600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:45890800-45891800	Enhancers	Brain Germinal Matrix	brain
37	chr6:45890800-45892200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:45891000-45898400	Weak transcription	Fetal Kidney	kidney
39	chr6:45891200-45891400	Enhancers	HMEC	breast
40	chr6:45891200-45891600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr6:45891200-45892800	Enhancers	Placenta	Placenta

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