Variant report

Variant	rs6425646
Chromosome Location	chr1:180510172-180510173
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	FOS	chr1:180509724-180510235	MCF10A-Er-Src	breast:	n/a	chr1:180509744-180509752
2	STAT3	chr1:180509854-180510249	MCF10A-Er-Src	breast:	n/a	chr1:180510033-180510044
3	FOSL2	chr1:180509796-180510347	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr1:180509799-180510284	SK-N-SH	brain:	n/a	n/a
5	FOS	chr1:180509833-180510215	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:180509807-180510214	MCF10A-Er-Src	breast:	n/a	chr1:180510033-180510044
7	PBX3	chr1:180509774-180510307	SK-N-SH	brain:	n/a	n/a
8	STAT3	chr1:180509885-180510210	MCF10A-Er-Src	breast:	n/a	chr1:180510033-180510044
9	TCF12	chr1:180509775-180510373	SK-N-SH	brain:	n/a	chr1:180510034-180510042
10	FOS	chr1:180509900-180510181	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:180509864-180510209	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180507839..180510458-chr1:180510629..180513153,2	K562	blood:
2	chr1:180505455..180510458-chr1:180510629..180513153,4	K562	blood:
3	chr1:180509296..180511935-chr1:180795313..180796906,2	K562	blood:
4	chr1:180505841..180513650-chr1:180514886..180521271,14	K562	blood:
5	chr1:180508398..180510494-chr1:180524364..180527463,3	K562	blood:
6	chr1:180506368..180508782-chr1:180508840..180510535,2	K562	blood:
7	chr1:180508149..180510326-chr1:180600706..180603079,2	K562	blood:
8	chr1:180497440..180500935-chr1:180506480..180510504,4	K562	blood:
9	chr1:180470492..180472995-chr1:180509075..180511111,2	MCF-7	breast:

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

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10913975	0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10913977	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10914021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10914022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10914035	0.95[EUR][1000 genomes]
rs10914036	0.81[CEU][hapmap]
rs10914038	0.94[EUR][1000 genomes]
rs12027839	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12027878	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12039331	0.86[CEU][hapmap]
rs12044653	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12045365	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12403226	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs12407684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12409923	0.81[ASN][1000 genomes]
rs13374665	1.00[CEU][hapmap]
rs13376342	0.80[EUR][1000 genomes]
rs1416822	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16856127	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[EUR][1000 genomes]
rs17300340	1.00[CEU][hapmap]
rs17300579	1.00[CEU][hapmap]
rs17300600	1.00[CEU][hapmap]
rs17300712	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17372295	1.00[CEU][hapmap]
rs17372362	1.00[CEU][hapmap]
rs17372667	0.80[EUR][1000 genomes]
rs2877481	0.83[ASN][1000 genomes]
rs4405110	1.00[CEU][hapmap]
rs4446932	0.86[EUR][1000 genomes]
rs4651065	0.80[EUR][1000 genomes]
rs4652509	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57537558	0.86[EUR][1000 genomes]
rs58047798	0.86[EUR][1000 genomes]
rs58089956	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59022209	0.80[EUR][1000 genomes]
rs60927564	0.85[EUR][1000 genomes]
rs61388681	0.81[EUR][1000 genomes]
rs6425643	0.84[EUR][1000 genomes]
rs6684596	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs6694454	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697232	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72716625	0.80[EUR][1000 genomes]
rs72716629	0.80[EUR][1000 genomes]
rs72716632	0.80[EUR][1000 genomes]
rs72720914	0.86[EUR][1000 genomes]
rs7513944	0.81[CEU][hapmap]
rs7517775	1.00[CEU][hapmap]
rs7525689	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541993	0.82[CEU][hapmap]
rs7546119	0.81[CEU][hapmap]
rs7547266	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551178	0.82[CEU][hapmap]
rs946631	0.81[CEU][hapmap]
rs946636	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs961162	0.85[EUR][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	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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
2	chr1:180497800-180511200	Weak transcription	Aorta	Aorta
3	chr1:180500000-180511200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:180503600-180510200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:180506200-180513200	Weak transcription	Pancreas	Pancrea
6	chr1:180506400-180511200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:180506600-180511200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:180506800-180511400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180507000-180514800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:180508000-180510200	Enhancers	Right Atrium	heart
11	chr1:180508000-180513200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:180508200-180510200	Enhancers	Right Ventricle	heart
13	chr1:180508800-180510400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180508800-180511400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:180508800-180513000	Enhancers	Fetal Heart	heart
16	chr1:180509000-180510600	Enhancers	Left Ventricle	heart
17	chr1:180509000-180511600	Enhancers	HMEC	breast
18	chr1:180509400-180511400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:180509400-180512800	Enhancers	Osteobl	bone
20	chr1:180509400-180513400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:180509600-180510400	Enhancers	HSMM	muscle
22	chr1:180509600-180510600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:180509600-180510600	Enhancers	Adipose Nuclei	Adipose
24	chr1:180509600-180510800	Enhancers	NH-A	brain
25	chr1:180509600-180512200	Enhancers	HSMMtube	muscle
26	chr1:180510000-180510200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:180510000-180510200	Enhancers	Fetal Muscle Trunk	muscle
28	chr1:180510000-180512200	Enhancers	K562	blood

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