Variant report

Variant	rs9548883
Chromosome Location	chr13:40265906-40265907
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	chr13:40263482..40266386-chr13:40274565..40277174,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10162010	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10467367	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs10467368	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4132636	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4132637	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4254189	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4261404	0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4275735	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4277227	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4294679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4300508	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4306389	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4321067	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4334152	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4363738	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4368051	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4432137	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs4457870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4485233	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4492929	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4514547	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4551909	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4556673	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4566029	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4569133	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4586300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4598779	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4606581	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4636783	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4941940	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4943688	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4943689	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4943692	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563737	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6563738	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6563739	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6563740	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7320424	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7324826	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7325354	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7326555	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7326699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7327674	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7330016	0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7330515	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs74044148	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7991151	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7991758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7993729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7994665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7998582	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7999758	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9315723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9315724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532417	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9548872	0.95[ASN][1000 genomes]
rs9548873	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9548876	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.95[ASN][1000 genomes]
rs9548877	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9548878	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548881	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9548884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9548885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566469	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9594362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603589	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9603591	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9603602	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548883	COG6	cis	Muscle Skeletal	GTEx
rs9548883	COG6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
2	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
6	chr13:40231600-40270200	Weak transcription	Gastric	stomach
7	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
9	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
10	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
11	chr13:40253000-40266200	Weak transcription	Colon Smooth Muscle	Colon
12	chr13:40253400-40266600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr13:40255000-40266600	Weak transcription	Fetal Stomach	stomach
14	chr13:40255000-40268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:40255000-40270000	Weak transcription	Lung	lung
16	chr13:40255000-40291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr13:40255200-40272800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:40255200-40291000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:40255400-40266800	Weak transcription	NHLF	lung
21	chr13:40255400-40272800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:40255600-40266800	Weak transcription	Brain Angular Gyrus	brain
23	chr13:40255600-40270800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:40255600-40272800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:40255600-40283600	Weak transcription	Fetal Brain Male	brain
26	chr13:40255800-40266600	Weak transcription	Brain Hippocampus Middle	brain
27	chr13:40255800-40271000	Weak transcription	Ovary	ovary
28	chr13:40255800-40283800	Weak transcription	Brain Anterior Caudate	brain
29	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
30	chr13:40257600-40274600	Weak transcription	HMEC	breast
31	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
32	chr13:40257800-40269200	Weak transcription	Fetal Kidney	kidney
33	chr13:40257800-40273200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr13:40258200-40266600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:40258200-40289800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:40262000-40271200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr13:40262600-40294000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr13:40262800-40266600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:40262800-40266600	Weak transcription	Fetal Lung	lung
40	chr13:40262800-40266800	Weak transcription	Brain Substantia Nigra	brain
41	chr13:40262800-40266800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr13:40262800-40269000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr13:40262800-40270600	Weak transcription	Primary T cells from cord blood	blood
44	chr13:40262800-40270600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:40262800-40272800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:40262800-40272800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr13:40262800-40273600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr13:40262800-40279200	Weak transcription	HepG2	liver
49	chr13:40262800-40285600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr13:40262800-40286800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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