Variant report

Variant	rs7976497
Chromosome Location	chr12:121135467-121135468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121122674..121127779-chr12:121131254..121137297,11	MCF-7	breast:
2	chr12:120973210..120975541-chr12:121135063..121137387,2	K562	blood:
3	chr12:121132775..121135777-chr12:121136647..121140338,4	MCF-7	breast:
4	chr12:121122826..121126231-chr12:121135368..121138328,4	MCF-7	breast:
5	chr12:121133471..121136112-chr12:121146959..121149468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000022840	Chromatin interaction
ENSG00000175970	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000256364	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10431385	0.82[EUR][1000 genomes]
rs10774566	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11065200	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11065223	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464515	0.93[ASN][1000 genomes]
rs1464516	0.92[ASN][1000 genomes]
rs17847	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1814851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005455	0.82[EUR][1000 genomes]
rs2138249	0.92[ASN][1000 genomes]
rs2140093	0.93[ASN][1000 genomes]
rs2239760	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2393749	0.89[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs3794214	0.91[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3794215	0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3829290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3914	0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs3915	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs504403	0.81[MKK][hapmap]
rs548093	0.90[EUR][1000 genomes]
rs555404	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556001	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs575437	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6490300	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs658521	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs695948	0.90[EUR][1000 genomes]
rs695949	0.93[EUR][1000 genomes]
rs695952	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs696337	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs696339	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs696340	0.89[EUR][1000 genomes]
rs697854	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs708783	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308648	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7312316	0.89[EUR][1000 genomes]
rs7964786	0.89[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs7978125	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs998727	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7976497	DYNLL1	cis	cerebellum	SCAN
rs7976497	UNC119B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121127600-121147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:121130200-121143000	Strong transcription	Dnd41	blood
3	chr12:121130200-121143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:121130400-121135800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:121130400-121136200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr12:121130400-121136400	Strong transcription	Primary B cells from cord blood	blood
7	chr12:121130600-121136000	Genic enhancers	Fetal Intestine Large	intestine
8	chr12:121130600-121136000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:121130600-121141800	Strong transcription	NHEK	skin
10	chr12:121130600-121142000	Strong transcription	Fetal Stomach	stomach
11	chr12:121130600-121142400	Strong transcription	GM12878-XiMat	blood
12	chr12:121130600-121143200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:121130800-121135600	Strong transcription	Spleen	Spleen
14	chr12:121130800-121136000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:121130800-121136000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:121130800-121140000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:121130800-121140400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:121130800-121141600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr12:121130800-121141800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:121130800-121141800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:121130800-121141800	Strong transcription	Thymus	Thymus
22	chr12:121130800-121142000	Strong transcription	Osteobl	bone
23	chr12:121130800-121142200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:121130800-121143600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:121131000-121135600	Strong transcription	Aorta	Aorta
26	chr12:121131000-121139800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:121131000-121141200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:121131000-121141600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:121131000-121142400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:121131200-121136000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:121131200-121136200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:121131200-121136200	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:121131200-121137400	Strong transcription	Gastric	stomach
34	chr12:121131200-121141400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:121131200-121141800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:121131200-121141800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:121131200-121142000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:121131200-121143800	Strong transcription	Fetal Thymus	thymus
39	chr12:121131400-121136400	Strong transcription	Pancreas	Pancrea
40	chr12:121131400-121140200	Strong transcription	K562	blood
41	chr12:121131400-121141000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr12:121131400-121141800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:121131400-121142200	Strong transcription	Primary T cells from cord blood	blood
44	chr12:121131600-121136400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:121131600-121136600	Strong transcription	NHDF-Ad	bronchial
46	chr12:121131600-121138200	Strong transcription	Hela-S3	cervix
47	chr12:121131600-121140000	Strong transcription	Ovary	ovary
48	chr12:121131600-121141200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr12:121131600-121141800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:121131600-121141800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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