Variant report

Variant	rs6580809
Chromosome Location	chr12:51609600-51609601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51545382..51548232-chr12:51608906..51610842,2	K562	blood:
2	chr12:51475900..51479120-chr12:51609514..51613581,8	MCF-7	breast:
3	chr12:51474480..51479024-chr12:51609420..51613050,8	MCF-7	breast:
4	chr12:51595711..51598749-chr12:51608220..51613018,6	K562	blood:
5	chr12:51609133..51616659-chr12:51628963..51635200,14	K562	blood:
6	chr12:51563450..51568971-chr12:51609008..51613972,14	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000135457	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10431487	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10735832	0.83[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10783422	0.87[EUR][1000 genomes]
rs10783423	0.86[EUR][1000 genomes]
rs10783425	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs10876154	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876155	0.87[EUR][1000 genomes]
rs11169761	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1130598	0.86[EUR][1000 genomes]
rs3888223	0.85[EUR][1000 genomes]
rs61932928	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6421171	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs6580816	0.83[EUR][1000 genomes]
rs6580817	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs7305016	0.92[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs7307217	0.87[EUR][1000 genomes]
rs7314235	0.86[EUR][1000 genomes]
rs7398443	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959901	0.86[EUR][1000 genomes]
rs7975737	0.87[ASN][1000 genomes]
rs7976292	0.88[ASN][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	nsv558876	chr12:51591367-51612730	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580809	SPATS2	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51567400-51610600	Weak transcription	Right Atrium	heart
2	chr12:51581400-51610200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:51581800-51610600	Weak transcription	Colonic Mucosa	Colon
4	chr12:51584400-51610800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:51585000-51610200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:51585000-51610800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:51585400-51610200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:51585800-51610400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:51586000-51610200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:51586400-51610200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:51590800-51610400	Weak transcription	HSMMtube	muscle
12	chr12:51592400-51610200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:51592400-51610600	Weak transcription	Pancreas	Pancrea
14	chr12:51592400-51610800	Weak transcription	Esophagus	oesophagus
15	chr12:51592800-51610200	Weak transcription	Right Ventricle	heart
16	chr12:51592800-51610400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:51593200-51610200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:51594400-51610400	Weak transcription	Liver	Liver
19	chr12:51595200-51610800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:51595600-51610400	Weak transcription	NH-A	brain
21	chr12:51596000-51610200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:51597400-51610200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:51597400-51610200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:51597400-51611000	Weak transcription	Primary T cells from cord blood	blood
25	chr12:51597600-51610400	Weak transcription	Fetal Lung	lung
26	chr12:51597800-51610000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:51597800-51610000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:51597800-51610400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:51598000-51610200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:51598000-51610200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:51598000-51610200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:51598000-51610400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:51598000-51610400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:51598200-51610400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:51598200-51610600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:51598200-51610600	Weak transcription	Gastric	stomach
37	chr12:51598400-51610400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:51598400-51610400	Weak transcription	Ovary	ovary
39	chr12:51598800-51610000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:51598800-51610200	Weak transcription	Adipose Nuclei	Adipose
41	chr12:51599400-51610400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:51599400-51610600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:51601600-51610200	Weak transcription	Osteobl	bone
44	chr12:51601600-51610600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr12:51602400-51610400	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:51602400-51610600	Weak transcription	Left Ventricle	heart
47	chr12:51604400-51610600	Weak transcription	Small Intestine	intestine
48	chr12:51604800-51610200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:51604800-51610600	Weak transcription	Aorta	Aorta
50	chr12:51604800-51610600	Weak transcription	Lung	lung

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