Variant report

Variant	rs2150231
Chromosome Location	chr6:4490480-4490481
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	GATA3	chr6:4489756-4490803	MCF-7	breast:	n/a	chr6:4490476-4490484
2	NR2F2	chr6:4489508-4490659	MCF-7	breast:	n/a	n/a
3	GATA3	chr6:4489536-4490870	MCF-7	breast:	n/a	chr6:4490476-4490484
4	TCF12	chr6:4489586-4490797	MCF-7	breast:	n/a	chr6:4490031-4490040
5	GATA3	chr6:4489469-4490718	MCF-7	breast:	n/a	chr6:4490476-4490484
6	FOXM1	chr6:4489639-4490923	MCF-7	breast:	n/a	n/a
7	HDAC2	chr6:4489633-4490727	MCF-7	breast:	n/a	chr6:4490476-4490485 chr6:4490612-4490621
8	TCF7L2	chr6:4489646-4490594	MCF-7	breast:	n/a	chr6:4489961-4489975
9	TCF12	chr6:4489512-4490874	MCF-7	breast:	n/a	chr6:4490031-4490040
10	MAX	chr6:4489828-4490742	MCF-7	breast:	n/a	n/a
11	EP300	chr6:4489655-4490813	MCF-7	breast:	n/a	chr6:4490612-4490622 chr6:4490030-4490040 chr6:4489725-4489732
12	EP300	chr6:4489675-4490742	MCF-7	breast:	n/a	chr6:4490612-4490622 chr6:4490030-4490040 chr6:4489725-4489732
13	ZNF217	chr6:4489704-4490652	MCF-7	breast:	n/a	n/a
14	NR2F2	chr6:4489609-4490869	MCF-7	breast:	n/a	n/a
15	MYC	chr6:4490299-4490519	MCF-7	breast:	n/a	n/a
16	SIN3AK20	chr6:4489425-4490949	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4476053..4476701-chr6:4489878..4490608,2	MCF-7	breast:
2	chr6:4490287..4491939-chr6:4601250..4603632,2	MCF-7	breast:
3	chr6:4488176..4491651-chr6:4775983..4779929,5	MCF-7	breast:
4	chr6:4488735..4490606-chr6:4493086..4495998,2	MCF-7	breast:
5	chr6:4489721..4491825-chr6:4493437..4495768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260239	TF binding region
ENSG00000153046	Chromatin interaction
ENSG00000260673	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1009602	0.92[ASN][1000 genomes]
rs1009603	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1009604	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1011087	0.81[ASN][1000 genomes]
rs1011088	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1011089	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1265245	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1265250	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1265256	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1265259	0.81[ASN][1000 genomes]
rs1265260	0.81[ASN][1000 genomes]
rs13195445	0.81[ASN][1000 genomes]
rs1571630	0.81[ASN][1000 genomes]
rs2181015	0.82[JPT][hapmap]
rs3929704	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959295	0.81[ASN][1000 genomes]
rs4959296	0.81[ASN][1000 genomes]
rs4959297	0.81[ASN][1000 genomes]
rs4959299	0.84[ASN][1000 genomes]
rs4959989	0.81[ASN][1000 genomes]
rs4959990	0.81[ASN][1000 genomes]
rs4959991	0.81[ASN][1000 genomes]
rs4959992	0.81[ASN][1000 genomes]
rs4959993	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4959994	0.82[ASN][1000 genomes]
rs4959995	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959997	1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs4959998	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs62384876	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914063	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6930327	0.80[ASN][1000 genomes]
rs878780	0.84[AMR][1000 genomes]
rs911565	0.80[ASN][1000 genomes]
rs9378883	0.89[ASN][1000 genomes]
rs9392053	0.81[ASN][1000 genomes]
rs9405748	0.81[ASN][1000 genomes]
rs9502189	0.81[ASN][1000 genomes]
rs9504123	0.81[ASN][1000 genomes]
rs9504124	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv970369	chr6:4481968-4554947	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4489400-4490800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr6:4490000-4490600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:4490000-4491000	Enhancers	Esophagus	oesophagus
4	chr6:4490000-4492400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:4490400-4492600	Enhancers	Placenta	Placenta

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