Variant report

Variant	rs4839296
Chromosome Location	chr1:113693396-113693397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113686049..113694370-chr1:113929775..113935752,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10442680	0.80[EUR][1000 genomes]
rs10494148	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10494149	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10494150	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10494152	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10494153	0.80[EUR][1000 genomes]
rs10776764	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11102590	0.90[EUR][1000 genomes]
rs11102591	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133524	0.83[AMR][1000 genomes]
rs12070586	0.91[EUR][1000 genomes]
rs12072108	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs12073607	0.91[EUR][1000 genomes]
rs12123070	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12123194	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12123876	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125209	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12125253	0.87[EUR][1000 genomes]
rs12125281	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125282	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12126040	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12126180	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12126412	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12126415	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12127119	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12127186	0.93[EUR][1000 genomes]
rs12129741	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12129773	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12129924	0.87[EUR][1000 genomes]
rs12130429	0.87[EUR][1000 genomes]
rs12130787	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12131406	0.85[EUR][1000 genomes]
rs12132547	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12133159	0.85[EUR][1000 genomes]
rs12133521	0.85[EUR][1000 genomes]
rs12134261	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12134347	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12136369	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12137440	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12140812	0.80[EUR][1000 genomes]
rs12141374	0.87[EUR][1000 genomes]
rs12141890	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs1216791	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216796	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216797	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216872	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1216873	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1216878	0.80[EUR][1000 genomes]
rs1216879	0.80[EUR][1000 genomes]
rs1216880	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1216881	0.80[EUR][1000 genomes]
rs1216882	0.80[EUR][1000 genomes]
rs1216884	0.85[EUR][1000 genomes]
rs1216885	0.83[AMR][1000 genomes]
rs1216886	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs1216889	0.82[AMR][1000 genomes]
rs1216890	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs12404563	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405087	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723657	0.87[EUR][1000 genomes]
rs12728957	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12732564	0.86[EUR][1000 genomes]
rs12736831	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12745847	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748429	0.87[EUR][1000 genomes]
rs12757593	0.90[EUR][1000 genomes]
rs12760482	0.87[EUR][1000 genomes]
rs1316767	0.87[EUR][1000 genomes]
rs1324893	0.80[EUR][1000 genomes]
rs1661	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs17031099	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs17031158	0.87[EUR][1000 genomes]
rs17031160	0.87[EUR][1000 genomes]
rs17497065	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1933656	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933660	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1999905	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1999906	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2185105	0.87[EUR][1000 genomes]
rs2185106	0.87[EUR][1000 genomes]
rs2359709	0.86[EUR][1000 genomes]
rs2359710	0.87[EUR][1000 genomes]
rs2359711	0.87[EUR][1000 genomes]
rs34236373	0.87[EUR][1000 genomes]
rs34441710	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35368423	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35470019	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35737003	0.84[EUR][1000 genomes]
rs35793987	0.91[EUR][1000 genomes]
rs35822819	0.85[EUR][1000 genomes]
rs36049267	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240536	0.91[EUR][1000 genomes]
rs4427400	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4630126	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs4839290	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839293	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4839295	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839297	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56204018	0.91[EUR][1000 genomes]
rs6537773	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537777	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6683099	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67028986	0.93[EUR][1000 genomes]
rs67038449	0.93[EUR][1000 genomes]
rs72685622	0.91[EUR][1000 genomes]
rs749956	0.87[EUR][1000 genomes]
rs7513596	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7513698	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7515810	0.87[EUR][1000 genomes]
rs7521854	0.86[EUR][1000 genomes]
rs7540970	0.87[EUR][1000 genomes]
rs7542423	0.80[EUR][1000 genomes]
rs7543653	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7548091	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7551138	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7556148	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs7556534	0.85[EUR][1000 genomes]
rs946219	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs946220	0.80[EUR][1000 genomes]
rs9628702	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
7	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113686200-113695600	Weak transcription	Stomach Mucosa	stomach
2	chr1:113690000-113695600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:113690800-113694200	Weak transcription	HepG2	liver
4	chr1:113691000-113695600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:113691000-113695600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:113691000-113695600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:113692200-113698600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:113692800-113693600	Enhancers	GM12878-XiMat	blood
9	chr1:113693200-113693400	Enhancers	HUES48 Cell Line	embryonic stem cell

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