Variant report

Variant	rs6488527
Chromosome Location	chr12:12589154-12589155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12588163..12590134-chr12:12591817..12594282,2	K562	blood:
2	chr12:12583518..12585650-chr12:12588474..12590636,2	K562	blood:
3	chr12:12587508..12589522-chr12:12868526..12870238,2	MCF-7	breast:
4	chr12:12588493..12590525-chr12:12592316..12593920,2	MCF-7	breast:
5	chr12:12586894..12590134-chr12:12591817..12594282,3	K562	blood:

Variant related genes	Relation type
ENSG00000111276	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11831188	1.00[ASN][1000 genomes]
rs11831555	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16908006	0.85[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16908019	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17312912	1.00[JPT][hapmap]
rs1861674	0.93[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2193270	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs4763288	1.00[JPT][hapmap]
rs4763289	1.00[JPT][hapmap]
rs4763824	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763827	1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763831	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs56261569	0.81[ASN][1000 genomes]
rs58218344	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58529509	1.00[ASN][1000 genomes]
rs60022096	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60363317	1.00[ASN][1000 genomes]
rs60971404	1.00[ASN][1000 genomes]
rs6488521	1.00[ASN][1000 genomes]
rs6488523	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133988	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7134787	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7135655	0.83[GIH][hapmap]
rs714480	1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7306292	1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7309982	0.83[GIH][hapmap]
rs73287587	1.00[ASN][1000 genomes]
rs7957014	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973069	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975061	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7978842	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7980390	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888198	0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6488527	LOH12CR1	cis	cerebellum	SCAN
rs6488527	CLEC6A	cis	parietal	SCAN
rs6488527	EPS8	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12578800-12589200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:12582000-12589200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:12582600-12592000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:12582600-12595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:12582600-12599400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:12582800-12592600	Weak transcription	NH-A	brain
7	chr12:12582800-12596400	Weak transcription	Spleen	Spleen
8	chr12:12583000-12589400	Weak transcription	HSMM	muscle
9	chr12:12583000-12594000	Weak transcription	HSMMtube	muscle
10	chr12:12584000-12598600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:12584200-12589200	Enhancers	Fetal Lung	lung
12	chr12:12584200-12590200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:12584200-12592200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:12584200-12592800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:12584200-12593200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:12584400-12592000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:12585400-12593200	Weak transcription	Small Intestine	intestine
18	chr12:12585600-12589200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:12585600-12590200	Weak transcription	HMEC	breast
20	chr12:12585600-12592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:12585600-12592000	Weak transcription	HUVEC	blood vessel
22	chr12:12585600-12595200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:12585800-12595400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:12586000-12589200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:12586000-12589200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:12586000-12589400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:12586000-12593200	Weak transcription	Liver	Liver
28	chr12:12586000-12594200	Weak transcription	Hela-S3	cervix
29	chr12:12586000-12595000	Weak transcription	Adipose Nuclei	Adipose
30	chr12:12586200-12589200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:12586200-12595000	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:12586200-12595400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:12586600-12594200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:12586800-12590400	Weak transcription	Osteobl	bone
35	chr12:12586800-12594000	Weak transcription	Right Ventricle	heart
36	chr12:12587000-12589400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:12587000-12590800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:12587000-12591800	Weak transcription	NHEK	skin
39	chr12:12587000-12592200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:12587000-12592600	Weak transcription	Stomach Mucosa	stomach
41	chr12:12587000-12593800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:12587000-12594800	Weak transcription	Aorta	Aorta
43	chr12:12587000-12594800	Weak transcription	Esophagus	oesophagus
44	chr12:12587000-12594800	Weak transcription	Placenta	Placenta
45	chr12:12587200-12593200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:12587200-12593800	Weak transcription	Fetal Intestine Small	intestine
47	chr12:12587200-12594000	Weak transcription	Brain Angular Gyrus	brain
48	chr12:12587200-12594000	Weak transcription	Lung	lung
49	chr12:12587200-12594000	Weak transcription	Psoas Muscle	Psoas
50	chr12:12587200-12594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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