Variant report

Variant	rs775648
Chromosome Location	chr12:67749482-67749483
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67749207..67750098-chr12:67807487..67808078,2	MCF-7	breast:
2	chr12:67748977..67750721-chr12:67808924..67810115,20	MCF-7	breast:
3	chr12:67749335..67750320-chr12:67808991..67809898,13	MCF-7	breast:
4	chr12:67748303..67751189-chr12:68042035..68043967,2	MCF-7	breast:
5	chr12:67661958..67663624-chr12:67746766..67749634,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111530	Chromatin interaction
ENSG00000127334	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1066387	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1066388	0.94[AFR][1000 genomes]
rs1066394	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1066395	0.94[AFR][1000 genomes]
rs10784625	0.82[ASW][hapmap];0.90[CEU][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap]
rs1082701	0.94[AFR][1000 genomes]
rs1082702	0.94[AFR][1000 genomes]
rs1082708	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1082709	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1082711	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1092475	0.81[AMR][1000 genomes]
rs11176678	0.82[ASW][hapmap];0.90[CEU][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap]
rs1143758	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1143947	1.00[AFR][1000 genomes]
rs1143948	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1152900	0.82[AFR][1000 genomes]
rs1161088	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1177317	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252404	0.87[AFR][1000 genomes]
rs1252406	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1252408	0.87[AFR][1000 genomes]
rs1252410	0.87[AFR][1000 genomes]
rs1252414	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252418	0.82[AFR][1000 genomes]
rs1252423	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1272090	0.94[AFR][1000 genomes]
rs1658780	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1985475	0.90[CEU][hapmap]
rs2870938	0.81[ASN][1000 genomes]
rs4143175	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6581753	0.82[ASN][1000 genomes]
rs710622	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs710623	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs710624	0.87[AFR][1000 genomes]
rs710798	0.91[AFR][1000 genomes]
rs710801	1.00[AFR][1000 genomes]
rs7310645	0.82[ASN][1000 genomes]
rs7316350	0.82[ASN][1000 genomes]
rs775307	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs775308	0.87[AFR][1000 genomes]
rs775310	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs775624	0.87[AFR][1000 genomes]
rs775628	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs775634	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs775646	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775647	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775650	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs775653	1.00[AFR][1000 genomes]
rs775654	1.00[AFR][1000 genomes]
rs775656	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs775657	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs775659	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs775661	0.87[AFR][1000 genomes]
rs775662	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7959649	0.84[ASN][1000 genomes]
rs796508	0.87[AFR][1000 genomes]
rs796521	0.82[YRI][hapmap]
rs800166	1.00[ASW][hapmap];0.90[CEU][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs800167	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs812325	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs812326	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs983630	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[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	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs775648	USP15	cis	cerebellum	SCAN
rs775648	HMGA2	cis	parietal	SCAN
rs775648	YEATS4	cis	cerebellum	SCAN
rs775648	CAND1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67733800-67761800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:67741800-67759200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:67748000-67750000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:67748000-67750200	Enhancers	Fetal Lung	lung
5	chr12:67748000-67753600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:67748000-67753800	Enhancers	HSMM	muscle
7	chr12:67748200-67749800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:67748200-67750200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:67748200-67750200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:67748200-67750200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:67748200-67750200	Enhancers	NH-A	brain
12	chr12:67748200-67750400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:67748400-67749600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:67748400-67749600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:67748400-67749800	Weak transcription	Small Intestine	intestine
16	chr12:67748400-67751200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:67748400-67752200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:67748600-67749600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:67748600-67749800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:67748600-67750000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:67748600-67750400	Enhancers	Primary T cells from cord blood	blood
22	chr12:67748600-67752000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:67748600-67752200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:67748600-67752600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:67748600-67752600	Weak transcription	Right Atrium	heart
26	chr12:67748800-67749800	Weak transcription	Fetal Stomach	stomach
27	chr12:67748800-67750200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:67748800-67750400	Enhancers	Fetal Heart	heart
29	chr12:67748800-67750400	Enhancers	Rectal Smooth Muscle	rectum
30	chr12:67749000-67749600	Enhancers	Fetal Kidney	kidney
31	chr12:67749000-67750000	Weak transcription	Psoas Muscle	Psoas
32	chr12:67749000-67750200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:67749000-67750400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr12:67749000-67751600	Weak transcription	Left Ventricle	heart
35	chr12:67749200-67750200	Flanking Active TSS	HSMMtube	muscle
36	chr12:67749200-67750200	Enhancers	NHDF-Ad	bronchial
37	chr12:67749200-67750400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr12:67749200-67750400	Enhancers	Dnd41	blood
39	chr12:67749200-67750600	Enhancers	Adipose Nuclei	Adipose
40	chr12:67749400-67749600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr12:67749400-67749800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:67749400-67749800	Enhancers	HMEC	breast
43	chr12:67749400-67749800	Enhancers	NHEK	skin
44	chr12:67749400-67749800	Flanking Active TSS	Osteobl	bone
45	chr12:67749400-67750200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:67749400-67750200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:67749400-67751200	Active TSS	Skeletal Muscle Female	skeletal muscle

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