Variant report

Variant	rs17100642
Chromosome Location	chr12:65150526-65150527
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	RUNX3	chr12:65150080-65150529	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:65150244..65154683-chr12:65172497..65176188,8	MCF-7	breast:
2	chr12:65149391..65152875-chr12:65160057..65163271,3	K562	blood:
3	chr12:65148774..65157978-chr12:65171970..65176271,20	MCF-7	breast:
4	chr12:65144722..65146746-chr12:65149884..65152740,2	K562	blood:

Variant related genes	Relation type
ENSG00000215159	TF binding region
GNS	TF binding region
ENSG00000111490	Chromatin interaction
ENSG00000135677	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12815624	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100600	0.93[MKK][hapmap]
rs17100604	0.93[MKK][hapmap]
rs17100619	1.00[MEX][hapmap]
rs17100621	1.00[MEX][hapmap]
rs17100632	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100633	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60648839	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74099668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv899210	chr12:65076498-65184236	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65106400-65152600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:65125200-65152400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:65129800-65152400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:65132800-65152200	Weak transcription	Colonic Mucosa	Colon
5	chr12:65133800-65150800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:65136400-65152400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:65137000-65152400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:65137200-65152600	Weak transcription	Esophagus	oesophagus
9	chr12:65138200-65152000	Weak transcription	Psoas Muscle	Psoas
10	chr12:65138600-65152400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:65139000-65151600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:65139600-65151600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:65140200-65151200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:65140200-65151600	Weak transcription	K562	blood
15	chr12:65140200-65152200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:65141200-65151200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:65141200-65152400	Weak transcription	A549	lung
18	chr12:65141400-65150800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:65141400-65151400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:65141800-65151400	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:65142600-65151600	Weak transcription	NHEK	skin
22	chr12:65143800-65151600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:65143800-65151600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:65143800-65151600	Weak transcription	Fetal Brain Male	brain
25	chr12:65144000-65150800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:65144600-65151800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:65144600-65152200	Weak transcription	HSMMtube	muscle
28	chr12:65144800-65151200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:65144800-65151600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:65144800-65151600	Weak transcription	Brain Angular Gyrus	brain
31	chr12:65144800-65151600	Weak transcription	Brain Substantia Nigra	brain
32	chr12:65144800-65151600	Weak transcription	Fetal Brain Female	brain
33	chr12:65144800-65151600	Weak transcription	Pancreas	Pancrea
34	chr12:65144800-65151600	Weak transcription	NHLF	lung
35	chr12:65144800-65151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:65144800-65152000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:65144800-65152400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:65145000-65151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:65145000-65151600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:65145000-65151600	Weak transcription	Fetal Thymus	thymus
41	chr12:65145000-65151800	Weak transcription	Thymus	Thymus
42	chr12:65145400-65151600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:65145400-65151800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:65145400-65152400	Weak transcription	Fetal Kidney	kidney
45	chr12:65145600-65150800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:65145600-65151200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:65145600-65151400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:65145600-65151600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:65145600-65151800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:65145600-65151800	Weak transcription	HMEC	breast

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