Variant report

Variant	rs17379216
Chromosome Location	chr12:12674965-12674966
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	REST	chr12:12672087-12675366	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr12:12674723-12675295	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr12:12674936-12675332	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:12674702-12675171	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:12673127..12675193-chr12:12712366..12713939,3	MCF-7	breast:
2	chr12:12551031..12553032-chr12:12674320..12676066,2	MCF-7	breast:
3	chr12:12672853..12675163-chr12:12712393..12714277,2	K562	blood:
4	chr12:12672692..12674511-chr12:12674724..12676812,2	MCF-7	breast:

Variant related genes	Relation type
DUSP16	TF binding region
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10845553	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10845554	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10845557	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10845562	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845563	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs10845565	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845569	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11054925	0.83[ASN][1000 genomes]
rs11054926	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054935	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11609905	0.92[ASN][1000 genomes]
rs11612508	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12424448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12819116	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17312926	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2417191	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736107	0.88[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs747726	0.92[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs888197	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs962927	0.89[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv523366	chr12:12665246-12679124	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv33583	chr12:12665776-12679108	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv523022	chr12:12673551-12688181	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17379216	ETV6	cis	cerebellum	SCAN
rs17379216	LOH12CR1	cis	parietal	SCAN
rs17379216	AICDA	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
2	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
3	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:12659800-12678600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:12660000-12681800	Weak transcription	Fetal Kidney	kidney
7	chr12:12660400-12686200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:12660800-12676600	Weak transcription	Pancreas	Pancrea
9	chr12:12660800-12679800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:12664000-12690400	Weak transcription	NHLF	lung
11	chr12:12665000-12684400	Weak transcription	NHDF-Ad	bronchial
12	chr12:12665000-12685600	Weak transcription	HMEC	breast
13	chr12:12665000-12686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:12665800-12678800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:12666800-12681200	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:12667000-12675000	Weak transcription	Spleen	Spleen
17	chr12:12667400-12686400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:12667600-12680800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:12668000-12680800	Weak transcription	Right Atrium	heart
20	chr12:12670000-12677400	Enhancers	Stomach Mucosa	stomach
21	chr12:12671200-12676200	Weak transcription	Gastric	stomach
22	chr12:12671200-12677000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:12671200-12681200	Weak transcription	HUVEC	blood vessel
24	chr12:12671400-12686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:12671400-12686200	Weak transcription	Fetal Stomach	stomach
26	chr12:12671600-12675000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr12:12671600-12678600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:12671600-12680800	Weak transcription	Lung	lung
29	chr12:12672000-12678000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:12672400-12680600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:12672600-12677800	Weak transcription	HSMMtube	muscle
32	chr12:12672800-12691200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:12673000-12675400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr12:12673000-12676600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:12673000-12676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:12673000-12676600	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:12673000-12676600	Weak transcription	Right Ventricle	heart
38	chr12:12673000-12678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:12673000-12678600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:12673000-12679600	Weak transcription	Fetal Lung	lung
41	chr12:12673000-12680600	Weak transcription	Osteobl	bone
42	chr12:12673000-12680800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:12673000-12680800	Weak transcription	Ovary	ovary
44	chr12:12673000-12681200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:12673000-12685200	Weak transcription	NHEK	skin
46	chr12:12673000-12690200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:12673200-12675600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:12673200-12676200	Weak transcription	Fetal Heart	heart
49	chr12:12673200-12677000	Genic enhancers	HepG2	liver
50	chr12:12673200-12680800	Weak transcription	A549	lung

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