Variant report

Variant	rs2279964
Chromosome Location	chr12:64173011-64173012
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	chr12:64172589-64175771	SK-N-SH	brain:	n/a	n/a
2	MAZ	chr12:64172756-64174502	IMR90	lung:	n/a	chr12:64174158-64174171 chr12:64174160-64174167 chr12:64173548-64173558 chr12:64174162-64174169

No.	Distal block	Cell Line	Cell type
1	chr12:64172533..64176121-chr12:64194832..64198679,5	K562	blood:
2	chr12:64130174..64132619-chr12:64170875..64173477,2	MCF-7	breast:
3	chr12:64169219..64171015-chr12:64171694..64173534,2	MCF-7	breast:
4	chr12:64172395..64175865-chr12:64176316..64181928,12	K562	blood:
5	chr12:64172631..64179011-chr12:64187703..64190145,6	MCF-7	breast:
6	chr12:64172589..64175160-chr12:64189373..64193026,5	MCF-7	breast:
7	chr12:64172802..64174995-chr12:64236940..64239856,2	MCF-7	breast:

Variant related genes	Relation type
TMEM5	TF binding region
ENSG00000196935	Chromatin interaction
ENSG00000118600	Chromatin interaction
ENSG00000249753	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10784368	0.81[EUR][1000 genomes]
rs11175162	0.81[EUR][1000 genomes]
rs11175172	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175174	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12301671	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1876465	0.82[CEU][hapmap]
rs1983148	0.85[MKK][hapmap]
rs3791156	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7304120	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7313084	0.81[EUR][1000 genomes]
rs73313417	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs949955	0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs949956	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv899171	chr12:63916682-64202233	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv430514	chr12:63939733-64183598	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2279964	SRGAP1	cis	cerebellum	SCAN
rs2279964	TBK1	cis	cerebellum	SCAN
rs2279964	SLC16A7	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64158600-64173200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:64167400-64173200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:64172000-64173200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:64172600-64173200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:64172800-64173200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:64172800-64173200	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:64172800-64173200	Enhancers	Fetal Thymus	thymus
8	chr12:64172800-64173200	Enhancers	Gastric	stomach
9	chr12:64172800-64173200	Enhancers	Pancreas	Pancrea
10	chr12:64172800-64173400	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr12:64172800-64173600	Flanking Active TSS	Dnd41	blood
12	chr12:64172800-64174200	Active TSS	Fetal Kidney	kidney
13	chr12:64172800-64174400	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr12:64172800-64174400	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr12:64172800-64174600	Active TSS	Brain Anterior Caudate	brain
16	chr12:64172800-64175200	Active TSS	K562	blood
17	chr12:64173000-64173200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:64173000-64173200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr12:64173000-64173200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:64173000-64173200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:64173000-64173200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:64173000-64173200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:64173000-64173200	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr12:64173000-64173200	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr12:64173000-64173200	Enhancers	Fetal Intestine Small	intestine
26	chr12:64173000-64173200	Enhancers	Rectal Smooth Muscle	rectum
27	chr12:64173000-64173200	Flanking Active TSS	A549	lung
28	chr12:64173000-64173200	Active TSS	HMEC	breast
29	chr12:64173000-64173400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr12:64173000-64173400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:64173000-64173400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr12:64173000-64173400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr12:64173000-64173400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr12:64173000-64173400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:64173000-64173400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:64173000-64173400	Flanking Active TSS	Liver	Liver
37	chr12:64173000-64173400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr12:64173000-64173400	Active TSS	Right Atrium	heart
39	chr12:64173000-64173400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr12:64173000-64173400	Flanking Active TSS	Hela-S3	cervix
41	chr12:64173000-64173400	Flanking Active TSS	HepG2	liver
42	chr12:64173000-64173600	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr12:64173000-64173600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:64173000-64174200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:64173000-64174200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:64173000-64174200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr12:64173000-64174200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:64173000-64174200	Active TSS	Fetal Heart	heart
49	chr12:64173000-64174200	Active TSS	Fetal Lung	lung
50	chr12:64173000-64174200	Active TSS	Rectal Mucosa Donor 29	rectum

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