Variant report

Variant	rs9576894
Chromosome Location	chr13:40313048-40313049
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	chr13:40304256..40306773-chr13:40312127..40313886,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11147769	0.83[AFR][1000 genomes]
rs11618960	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17591231	0.83[AFR][1000 genomes]
rs4133063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245396	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4288869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4338665	0.83[AFR][1000 genomes]
rs4403927	0.83[AFR][1000 genomes]
rs4408422	0.92[AFR][1000 genomes]
rs4409964	0.83[AFR][1000 genomes]
rs4943694	0.89[AFR][1000 genomes]
rs4943695	0.84[AFR][1000 genomes]
rs4943696	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7319128	0.84[AFR][1000 genomes]
rs7325068	0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7327824	0.84[AFR][1000 genomes]
rs7330211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7334651	0.85[YRI][hapmap];0.92[AFR][1000 genomes]
rs7337585	0.83[AFR][1000 genomes]
rs7998641	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8000009	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315729	0.83[AFR][1000 genomes]
rs9315730	0.82[AFR][1000 genomes]
rs9532429	0.84[AFR][1000 genomes]
rs9548898	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548900	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9548901	0.85[YRI][hapmap];0.92[AFR][1000 genomes]
rs9548905	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548913	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548914	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548916	0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548917	0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9548918	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548919	0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548920	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548922	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548926	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9548927	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548928	0.84[AFR][1000 genomes]
rs9548929	0.83[AFR][1000 genomes]
rs9548930	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs9566474	0.84[AFR][1000 genomes]
rs9576891	0.90[AFR][1000 genomes]
rs9576892	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9576895	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576896	0.84[AFR][1000 genomes]
rs9576897	0.83[AFR][1000 genomes]
rs9576898	0.84[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9576894	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
2	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
5	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
6	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:40292000-40313400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr13:40292400-40314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
10	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
12	chr13:40294600-40327800	Weak transcription	NH-A	brain
13	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
14	chr13:40297800-40329800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:40298400-40314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:40299200-40327600	Weak transcription	Fetal Heart	heart
17	chr13:40300800-40314400	Weak transcription	Primary B cells from cord blood	blood
18	chr13:40302000-40328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:40302400-40314600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr13:40302600-40315800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr13:40303400-40314000	Weak transcription	NHLF	lung
22	chr13:40303800-40316000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:40304000-40328800	Weak transcription	Dnd41	blood
24	chr13:40304600-40340000	Weak transcription	Osteobl	bone
25	chr13:40306000-40313600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr13:40306400-40327400	Weak transcription	HUVEC	blood vessel
27	chr13:40306600-40325200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:40306800-40315000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr13:40307600-40329400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr13:40309200-40331400	Weak transcription	Stomach Mucosa	stomach
31	chr13:40309200-40334600	Weak transcription	HepG2	liver
32	chr13:40310000-40313800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:40310600-40315400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:40311200-40316200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:40311400-40324000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr13:40311400-40347200	Weak transcription	HSMM	muscle
37	chr13:40311600-40314400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:40311600-40316400	Weak transcription	NHDF-Ad	bronchial
39	chr13:40311600-40317600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:40311600-40324200	Weak transcription	Adipose Nuclei	Adipose
41	chr13:40311600-40326600	Weak transcription	Placenta	Placenta
42	chr13:40311600-40329400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:40311600-40331200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr13:40311600-40339800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr13:40311600-40340000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr13:40311800-40313400	Weak transcription	Fetal Brain Female	brain
47	chr13:40311800-40313400	Weak transcription	Thymus	Thymus
48	chr13:40311800-40314400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr13:40311800-40314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr13:40311800-40315200	Weak transcription	Fetal Kidney	kidney

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