Variant report

Variant	rs13209887
Chromosome Location	chr6:163271944-163271945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:162863816..162864618-chr6:163271757..163272511,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs13202482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208648	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210195	0.81[ASN][1000 genomes]
rs13216389	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1893539	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1954912	1.00[CHB][hapmap]
rs2023036	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2023037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2023038	0.83[ASN][1000 genomes]
rs2023041	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2187195	1.00[ASN][1000 genomes]
rs2803080	1.00[ASN][1000 genomes]
rs2803081	1.00[ASN][1000 genomes]
rs2803083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2803084	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2803088	1.00[ASN][1000 genomes]
rs2803089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2803090	1.00[ASN][1000 genomes]
rs2803091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2803093	1.00[ASN][1000 genomes]
rs2803099	1.00[CHB][hapmap]
rs2803107	1.00[ASN][1000 genomes]
rs2849511	0.83[ASN][1000 genomes]
rs2849514	1.00[ASN][1000 genomes]
rs2849518	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2849519	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2849520	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2849521	0.83[ASN][1000 genomes]
rs2849524	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2849525	0.83[ASN][1000 genomes]
rs2849527	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2849532	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2849533	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2849534	1.00[ASN][1000 genomes]
rs2849540	1.00[ASN][1000 genomes]
rs2849542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2849545	1.00[CHB][hapmap]
rs2849548	1.00[ASN][1000 genomes]
rs2849552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34044012	1.00[ASN][1000 genomes]
rs34912663	0.83[ASN][1000 genomes]
rs35303937	1.00[ASN][1000 genomes]
rs35626571	1.00[ASN][1000 genomes]
rs4129785	1.00[ASN][1000 genomes]
rs6925156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71567666	1.00[ASN][1000 genomes]
rs71567683	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71567684	0.98[EUR][1000 genomes]
rs71567685	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764309	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870232	chr6:162640581-163315481	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv917926	chr6:162646457-163609259	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1030546	chr6:162748287-163475085	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv538518	chr6:162748287-163475085	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv605159	chr6:162800156-163479507	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1022105	chr6:162817344-163320793	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1015507	chr6:162865145-163334779	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv886905	chr6:162928898-163284038	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv481962	chr6:163033886-163401583	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1015155	chr6:163095774-163361624	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1032968	chr6:163095774-163391548	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv529089	chr6:163129464-163516451	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv886914	chr6:163142272-163282067	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv605182	chr6:163166902-163280204	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1025098	chr6:163220003-163343558	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv984581	chr6:163235106-163294421	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv521563	chr6:163248589-163305426	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv605185	chr6:163248589-163305426	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv886915	chr6:163250778-163289067	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1024624	chr6:163266701-163410702	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr6:163267400-163275800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:163268200-163273200	Weak transcription	Pancreas	Pancrea
3	chr6:163270400-163273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:163270400-163274000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:163270400-163275800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:163270400-163275800	Weak transcription	Fetal Brain Male	brain
7	chr6:163270400-163277800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:163270600-163272000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:163270600-163272200	Enhancers	Brain Hippocampus Middle	brain
10	chr6:163270600-163273200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:163270600-163273400	Weak transcription	Brain Germinal Matrix	brain
12	chr6:163270600-163274000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:163270600-163274200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:163270600-163275600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:163270600-163275600	Weak transcription	Fetal Heart	heart
16	chr6:163270600-163275800	Weak transcription	Left Ventricle	heart
17	chr6:163271200-163273200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:163271400-163272000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:163271400-163272400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:163271400-163272400	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr6:163271600-163272000	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr6:163271600-163272200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:163271600-163272400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:163271600-163272400	Active TSS	Brain Anterior Caudate	brain
25	chr6:163271600-163273600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:163271800-163272000	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr6:163271800-163272200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:163271800-163277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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