Variant report

Variant	rs6425647
Chromosome Location	chr1:180513318-180513319
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	FOXA2	chr1:180513223-180513690	A549	lung:	n/a	n/a
2	ESR1	chr1:180513092-180513410	T-47D	breast:	n/a	n/a
3	FOXA1	chr1:180513222-180513545	T-47D	breast:	n/a	chr1:180513361-180513376
4	NFYB	chr1:180513207-180513353	GM12878	blood:	n/a	n/a
5	FOXA1	chr1:180513184-180513538	T-47D	breast:	n/a	chr1:180513361-180513376
6	CEBPB	chr1:180513262-180513378	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180511395..180514188-chr1:180783985..180786756,2	K562	blood:
2	chr1:180512434..180513990-chr1:180599840..180601494,2	MCF-7	breast:
3	chr1:180511669..180514906-chr1:180530245..180533112,3	K562	blood:
4	chr1:180505841..180513650-chr1:180514886..180521271,14	K562	blood:
5	chr1:180470537..180472654-chr1:180512131..180513964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266683	TF binding region
ENSG00000143324	Chromatin interaction
ENSG00000135847	Chromatin interaction
ENSG00000266683	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10157891	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10733004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10737343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737345	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753210	0.90[ASN][1000 genomes]
rs10753213	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753214	0.90[ASN][1000 genomes]
rs10753217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10798763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10798764	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913972	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10914011	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10914019	0.90[ASN][1000 genomes]
rs10914020	0.90[ASN][1000 genomes]
rs12027553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12077904	0.90[ASN][1000 genomes]
rs12144149	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12565152	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1339722	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1339723	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1339726	0.90[ASN][1000 genomes]
rs1361363	0.90[ASN][1000 genomes]
rs1361628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1556935	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1556938	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1591898	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1934411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1935283	0.90[ASN][1000 genomes]
rs1970401	0.84[AMR][1000 genomes]
rs2153327	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2153753	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2331739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2331742	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41267628	0.91[AMR][1000 genomes]
rs41267634	0.91[AMR][1000 genomes]
rs4259605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4281291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4304539	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4333819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4532796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4540612	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4609392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4651061	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4651063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4651066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4651067	0.90[ASN][1000 genomes]
rs4652501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4652502	0.90[EUR][1000 genomes]
rs4652506	0.90[ASN][1000 genomes]
rs4652510	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61809269	0.84[AMR][1000 genomes]
rs61809270	0.84[AMR][1000 genomes]
rs61809273	0.84[AMR][1000 genomes]
rs61809274	0.84[AMR][1000 genomes]
rs61809275	0.84[AMR][1000 genomes]
rs61809276	0.84[AMR][1000 genomes]
rs61811627	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61811628	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811630	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811631	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61811635	0.84[AMR][1000 genomes]
rs6425620	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425621	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425623	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425624	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425642	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664944	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665615	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6667478	0.90[ASN][1000 genomes]
rs6669304	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6677367	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678261	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6680754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6682067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6683484	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6684842	0.90[ASN][1000 genomes]
rs6687873	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691333	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7515052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7522928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7526743	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7529042	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7532972	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7542568	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543143	0.90[ASN][1000 genomes]
rs7546030	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7555087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs946633	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs946634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs946635	1.00[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180507000-180514800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:180509400-180513400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:180510200-180516000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:180510400-180529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:180511000-180513400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:180511200-180513400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:180511200-180513400	Enhancers	Brain Anterior Caudate	brain
8	chr1:180511600-180516200	Weak transcription	Psoas Muscle	Psoas
9	chr1:180511800-180521200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:180512000-180515800	Weak transcription	Left Ventricle	heart
11	chr1:180512200-180513400	Weak transcription	Aorta	Aorta
12	chr1:180512200-180516200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:180512200-180516600	Weak transcription	Fetal Brain Female	brain
14	chr1:180512200-180521200	Weak transcription	HSMMtube	muscle
15	chr1:180512400-180515800	Weak transcription	Right Atrium	heart
16	chr1:180512400-180517800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:180512600-180516200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:180512600-180516200	Weak transcription	Brain Germinal Matrix	brain
19	chr1:180512800-180513400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:180512800-180517600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:180513000-180513400	Weak transcription	Fetal Heart	heart
22	chr1:180513000-180518000	Weak transcription	Fetal Brain Male	brain
23	chr1:180513200-180513400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:180513200-180513400	Enhancers	Ovary	ovary
25	chr1:180513200-180513600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:180513200-180513600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:180513200-180513600	Enhancers	Lung	lung
28	chr1:180513200-180513600	Enhancers	Pancreas	Pancrea
29	chr1:180513200-180513600	Enhancers	Right Ventricle	heart
30	chr1:180513200-180517400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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