Variant report

Variant	rs775324
Chromosome Location	chr12:57924050-57924051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57921185..57924132-chr12:58144470..58146639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135446	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1148553	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148554	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148555	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1284465	0.87[EUR][1000 genomes]
rs1284605	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1299737	0.84[EUR][1000 genomes]
rs1629410	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1669294	0.84[EUR][1000 genomes]
rs1669296	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669297	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678537	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs1679368	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1709871	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs1709874	0.83[EUR][1000 genomes]
rs2127318	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620677	0.83[EUR][1000 genomes]
rs2620679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2672571	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap]
rs2928382	0.83[EUR][1000 genomes]
rs2943696	0.84[EUR][1000 genomes]
rs3782129	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825080	0.89[JPT][hapmap]
rs3847699	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474544	0.84[EUR][1000 genomes]
rs4760273	0.80[EUR][1000 genomes]
rs496245	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs511752	0.92[CEU][hapmap];0.88[YRI][hapmap]
rs542278	0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs697221	0.92[ASW][hapmap];0.92[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs703835	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703836	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs703837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs703838	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs703839	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7299631	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747340	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs775236	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs775237	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs775241	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs775323	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs776038	0.92[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs776039	0.84[EUR][1000 genomes]
rs7964074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796546	0.84[EUR][1000 genomes]
rs899653	0.81[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs9737891	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
8	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
10	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
11	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs775324	DCTN2	cis	Muscle Skeletal	GTEx
rs775324	KRT7	cis	cerebellum	SCAN
rs775324	ATF7	cis	cerebellum	SCAN
rs775324	ITGB7	cis	cerebellum	SCAN
rs775324	AVIL	cis	cerebellum	SCAN
rs775324	CALCOCO1	cis	cerebellum	SCAN
rs775324	KRT81	cis	parietal	SCAN
rs775324	ACVRL1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57918400-57929400	Strong transcription	Ovary	ovary
3	chr12:57918400-57929800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:57918600-57924400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:57918600-57925400	Weak transcription	Fetal Kidney	kidney
6	chr12:57918600-57925400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:57918600-57929000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:57918600-57929600	Strong transcription	Aorta	Aorta
9	chr12:57918600-57929600	Strong transcription	Rectal Smooth Muscle	rectum
10	chr12:57918600-57930400	Strong transcription	Lung	lung
11	chr12:57918600-57933600	Strong transcription	Brain Hippocampus Middle	brain
12	chr12:57918600-57934800	Strong transcription	Osteobl	bone
13	chr12:57918600-57936400	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr12:57918600-57939600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:57918800-57929000	Strong transcription	Small Intestine	intestine
16	chr12:57918800-57929400	Strong transcription	Gastric	stomach
17	chr12:57918800-57929600	Strong transcription	Brain Substantia Nigra	brain
18	chr12:57918800-57929600	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr12:57918800-57929800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:57918800-57929800	Strong transcription	Fetal Lung	lung
21	chr12:57918800-57930600	Strong transcription	Primary T cells from cord blood	blood
22	chr12:57918800-57933800	Strong transcription	NHEK	skin
23	chr12:57919000-57928800	Strong transcription	Colonic Mucosa	Colon
24	chr12:57919000-57929400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:57919000-57929400	Strong transcription	Esophagus	oesophagus
26	chr12:57919000-57929600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:57919000-57929600	Strong transcription	Liver	Liver
28	chr12:57919000-57929600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:57919000-57929800	Strong transcription	Spleen	Spleen
30	chr12:57919000-57930000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr12:57919000-57930000	Strong transcription	NHLF	lung
32	chr12:57919000-57931200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:57919000-57932000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:57919000-57935600	Strong transcription	Thymus	Thymus
35	chr12:57919000-57937400	Weak transcription	Right Atrium	heart
36	chr12:57919200-57928800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:57919200-57929000	Strong transcription	GM12878-XiMat	blood
38	chr12:57919200-57929800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:57919200-57934800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:57919200-57939600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:57919400-57929000	Strong transcription	Brain Anterior Caudate	brain
42	chr12:57919400-57929200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:57919400-57929400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:57919400-57929800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr12:57919400-57930600	Strong transcription	HMEC	breast
46	chr12:57919400-57933400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:57919400-57933400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:57919400-57934400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:57919400-57936200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:57919400-57936200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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