Variant report

Variant	rs6451218
Chromosome Location	chr5:35777426-35777427
allele	C/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	CTCF	chr5:35777340-35777490	AG10803	skin:	n/a	n/a
2	SMC3	chr5:35777354-35778122	Hela-S3	cervix:	n/a	chr5:35777903-35777917
3	CTCF	chr5:35777280-35777430	SAEC	small airway:	n/a	n/a
4	CTCF	chr5:35777369-35778289	SK-N-SH	brain:	n/a	chr5:35777902-35777918 chr5:35777901-35777919 chr5:35777904-35777917 chr5:35777905-35777912 chr5:35777903-35777924 chr5:35777904-35777917
5	CTCF	chr5:35777400-35777550	HPAF	blood vessel:	n/a	n/a
6	CTCF	chr5:35777383-35778193	MCF-7	breast:	n/a	chr5:35777902-35777918 chr5:35777901-35777919 chr5:35777904-35777917 chr5:35777905-35777912 chr5:35777903-35777924 chr5:35777904-35777917

No.	Distal block	Cell Line	Cell type
1	chr5:35777408..35778477-chr5:35922335..35923637,7	MCF-7	breast:
2	chr5:35775517..35778648-chr5:35922425..35925646,3	MCF-7	breast:
3	chr5:35777405..35778401-chr5:35924712..35925240,2	K562	blood:
4	chr5:35777376..35779167-chr5:35921282..35923743,2	MCF-7	breast:

Variant related genes	Relation type
SPEF2	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10037564	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10043724	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs10043734	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10044393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10941258	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs10941260	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11957963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12697350	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2201410	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869462	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869623	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62353695	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451213	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875940	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs6891098	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs716971	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7443063	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7447153	0.85[CHB][hapmap]
rs7705904	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710255	0.86[CEU][hapmap];0.84[CHB][hapmap]

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	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35771000-35781800	Weak transcription	Brain Anterior Caudate	brain
2	chr5:35772400-35780600	Weak transcription	HSMM	muscle
3	chr5:35772800-35778000	Weak transcription	Fetal Thymus	thymus
4	chr5:35772800-35778000	Weak transcription	Thymus	Thymus
5	chr5:35774600-35780800	Weak transcription	NHDF-Ad	bronchial
6	chr5:35774600-35781000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:35775000-35779600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:35776400-35777600	Enhancers	Hela-S3	cervix
9	chr5:35776800-35777600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:35776800-35780400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:35777000-35777600	Enhancers	Osteobl	bone
12	chr5:35777000-35778000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr5:35777000-35778000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:35777000-35778000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr5:35777000-35778200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:35777000-35780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:35777000-35780600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:35777000-35780800	Weak transcription	HUVEC	blood vessel
19	chr5:35777200-35778000	Enhancers	Primary T cells from cord blood	blood
20	chr5:35777200-35778400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:35777200-35780000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:35777200-35780400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr5:35777400-35777800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:35777400-35778000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:35777400-35778000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:35777400-35780600	Weak transcription	NHLF	lung

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