Variant report

Variant	rs6580820
Chromosome Location	chr12:51657425-51657426
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51610351..51612451-chr12:51655429..51657960,2	K562	blood:
2	chr12:51639155..51642440-chr12:51654128..51658049,5	MCF-7	breast:
3	chr12:51651947..51654045-chr12:51655444..51659174,3	K562	blood:
4	chr12:51631289..51634509-chr12:51656307..51658177,4	MCF-7	breast:
5	chr12:51655428..51658395-chr12:51663198..51666359,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10747609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783426	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783427	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10783428	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876156	0.82[CEU][hapmap]
rs10876157	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876159	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1130641	0.83[CEU][hapmap]
rs1362963	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs1877260	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1877261	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975004	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271821	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359449	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884709	0.90[ASN][1000 genomes]
rs3210837	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs3886185	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3951438	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4761814	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4761815	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4761935	1.00[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4761938	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761966	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4761969	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4761981	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761995	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7133314	0.80[CEU][hapmap]
rs7133495	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7136290	0.80[AMR][1000 genomes]
rs7296747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7304578	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7311434	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7316347	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7316569	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7957667	0.80[AMR][1000 genomes]
rs9325148	0.87[MEX][hapmap];0.82[AMR][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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580820	COL2A1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51638400-51662800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:51639800-51662800	Weak transcription	Fetal Stomach	stomach
3	chr12:51640200-51662800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:51640200-51662800	Weak transcription	Pancreas	Pancrea
5	chr12:51640400-51659000	Weak transcription	HMEC	breast
6	chr12:51640400-51661600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:51640600-51661800	Weak transcription	NH-A	brain
8	chr12:51641600-51663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:51642000-51662800	Weak transcription	NHLF	lung
10	chr12:51642200-51661000	Weak transcription	Colonic Mucosa	Colon
11	chr12:51642200-51662800	Weak transcription	Gastric	stomach
12	chr12:51642200-51662800	Weak transcription	Right Ventricle	heart
13	chr12:51642200-51663000	Weak transcription	Lung	lung
14	chr12:51642400-51659400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:51642400-51662800	Weak transcription	Primary B cells from cord blood	blood
16	chr12:51642600-51658000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:51642600-51659200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:51642600-51659800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:51642600-51662600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:51642800-51658800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:51643000-51662600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:51643200-51662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:51644800-51659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:51645000-51658800	Weak transcription	Dnd41	blood
25	chr12:51645200-51661800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:51647800-51659200	Weak transcription	Placenta	Placenta
27	chr12:51648800-51662600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:51649400-51661400	Weak transcription	Esophagus	oesophagus
29	chr12:51649400-51662800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:51649600-51659400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:51651000-51662800	Weak transcription	Liver	Liver
32	chr12:51651200-51659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:51651200-51660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:51651400-51662800	Weak transcription	Fetal Intestine Large	intestine
35	chr12:51652000-51657800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:51653400-51663400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:51654200-51662800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:51656200-51657600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:51656400-51657600	Enhancers	HUVEC	blood vessel
40	chr12:51656600-51657600	Enhancers	NHDF-Ad	bronchial
41	chr12:51656600-51658000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:51656600-51658200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:51656600-51659000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:51656800-51659000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:51656800-51660000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:51656800-51662800	Weak transcription	Ovary	ovary
47	chr12:51656800-51662800	Weak transcription	Spleen	Spleen
48	chr12:51657000-51658200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:51657000-51658200	Genic enhancers	NHEK	skin
50	chr12:51657000-51658800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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