Variant report

Variant	rs2694015
Chromosome Location	chr12:56124648-56124649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:56121169-56124795	SK-N-SH	brain:	n/a	chr12:56122967-56122976 chr12:56122965-56122974 chr12:56122967-56122976 chr12:56122965-56122974
2	REST	chr12:56121691-56124753	H1-neurons	neurons:	n/a	chr12:56121849-56121862 chr12:56122366-56122375 chr12:56122563-56122573 chr12:56123753-56123761 chr12:56124288-56124297 chr12:56124307-56124325

No.	Distal block	Cell Line	Cell type
1	chr12:56122088..56125310-chr12:56509016..56512267,4	MCF-7	breast:
2	chr12:56122770..56125786-chr12:56400050..56403264,3	K562	blood:
3	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
4	chr12:56088543..56091362-chr12:56123816..56126744,2	K562	blood:
5	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
6	chr12:56098994..56103683-chr12:56119699..56126107,8	MCF-7	breast:
7	chr12:56122193..56124805-chr12:56319367..56323067,7	K562	blood:
8	chr12:56122035..56125892-chr12:56210581..56213887,4	K562	blood:
9	chr12:56074050..56076493-chr12:56123343..56125140,3	MCF-7	breast:
10	chr12:56122869..56125030-chr12:56332847..56335271,2	K562	blood:
11	chr12:56120587..56125243-chr12:56320195..56323478,6	MCF-7	breast:
12	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RDH5-1	chr12:56123446-56124979	NONHSAT028680

Variant related genes	Relation type
CD63	TF binding region
ENSG00000170439	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000170473	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1466512	1.00[AMR][1000 genomes]
rs1681085	1.00[AMR][1000 genomes]
rs1725358	1.00[AMR][1000 genomes]
rs1871999	1.00[AMR][1000 genomes]
rs2449476	1.00[AMR][1000 genomes]
rs2462935	1.00[AFR][1000 genomes]
rs2462938	1.00[AMR][1000 genomes]
rs2694008	1.00[AMR][1000 genomes]
rs2887997	1.00[AMR][1000 genomes]
rs4759012	1.00[AMR][1000 genomes]
rs4759202	1.00[AMR][1000 genomes]
rs55884432	1.00[AMR][1000 genomes]
rs6581083	1.00[AMR][1000 genomes]
rs7294345	1.00[AMR][1000 genomes]
rs7310325	1.00[AMR][1000 genomes]
rs772250	1.00[AMR][1000 genomes]
rs772252	1.00[AMR][1000 genomes]
rs772253	1.00[AMR][1000 genomes]
rs772256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772259	1.00[AMR][1000 genomes]
rs772260	1.00[AMR][1000 genomes]
rs772261	1.00[AMR][1000 genomes]
rs7956337	1.00[AMR][1000 genomes]
rs7963379	1.00[AMR][1000 genomes]
rs812230	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56121200-56125200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:56121800-56125000	Active TSS	HSMM	muscle
3	chr12:56122200-56124800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:56123000-56124800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr12:56123000-56124800	Flanking Active TSS	NH-A	brain
6	chr12:56123200-56124800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:56123200-56125000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:56123600-56124800	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr12:56123600-56125000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:56123600-56125000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:56123800-56124800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:56123800-56124800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:56123800-56124800	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr12:56124000-56124800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56124000-56124800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr12:56124000-56124800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr12:56124000-56124800	Flanking Active TSS	Fetal Heart	heart
18	chr12:56124000-56125000	Flanking Active TSS	Osteobl	bone
19	chr12:56124000-56130800	Weak transcription	Aorta	Aorta
20	chr12:56124000-56131200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:56124200-56124800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:56124200-56124800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:56124200-56124800	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:56124200-56124800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:56124200-56124800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr12:56124200-56124800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:56124200-56124800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:56124200-56124800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr12:56124200-56124800	Flanking Active TSS	Fetal Brain Male	brain
30	chr12:56124200-56124800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr12:56124200-56125000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:56124200-56125000	Enhancers	Lung	lung
33	chr12:56124200-56125000	Flanking Active TSS	NHLF	lung
34	chr12:56124200-56125200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:56124400-56124800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:56124400-56124800	Enhancers	Primary T cells from cord blood	blood
37	chr12:56124400-56124800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:56124400-56124800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr12:56124400-56124800	Enhancers	Adipose Nuclei	Adipose
40	chr12:56124400-56124800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:56124400-56124800	Enhancers	Fetal Intestine Small	intestine
42	chr12:56124400-56124800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr12:56124400-56124800	Enhancers	GM12878-XiMat	blood
44	chr12:56124400-56125000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:56124400-56125000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:56124400-56125000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr12:56124400-56125000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:56124400-56125000	Enhancers	Fetal Lung	lung
49	chr12:56124400-56125000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr12:56124400-56125200	Enhancers	Primary T cells fromperipheralblood	blood

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