Variant report

Variant	rs1696466
Chromosome Location	chr12:58116397-58116398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58116328-58119086	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:58116335-58118479	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:58112700-58119120	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:58114798-58119096	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58116094..58117634-chr12:58133329..58135229,2	K562	blood:
2	chr12:57906816..57909799-chr12:58115546..58118135,2	K562	blood:
3	chr12:58112503..58116669-chr12:58128862..58132734,4	K562	blood:
4	chr12:58115495..58117239-chr12:58136525..58139362,3	K562	blood:
5	chr12:58086741..58089162-chr12:58114553..58116663,2	MCF-7	breast:
6	chr12:58099859..58102384-chr12:58116011..58117778,2	MCF-7	breast:
7	chr12:58104338..58106820-chr12:58115614..58118088,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257342	TF binding region
AGAP2-AS1	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000135439	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10082911	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783842	0.81[AMR][1000 genomes]
rs10783843	0.80[AMR][1000 genomes]
rs10783844	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10877001	0.81[ASN][1000 genomes]
rs10877006	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10877007	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10877008	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11172306	0.85[AMR][1000 genomes]
rs1633360	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1633361	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1678504	0.81[ASN][1000 genomes]
rs1689584	0.81[ASN][1000 genomes]
rs1689585	0.81[ASN][1000 genomes]
rs238516	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619441	0.81[ASN][1000 genomes]
rs2928062	0.81[ASN][1000 genomes]
rs2928064	0.82[ASN][1000 genomes]
rs3825078	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4760168	0.81[ASN][1000 genomes]
rs701006	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs701008	0.81[ASN][1000 genomes]
rs7976852	0.86[AMR][1000 genomes]
rs7979246	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1696466	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1696466	FAM119B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58091200-58116600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:58098400-58117600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:58103400-58116400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:58106200-58116800	Strong transcription	Fetal Intestine Small	intestine
6	chr12:58106200-58120000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:58106800-58116600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:58108000-58116800	Strong transcription	Spleen	Spleen
9	chr12:58110000-58119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:58112200-58119600	Weak transcription	NHDF-Ad	bronchial
11	chr12:58113200-58116600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:58113200-58117400	Weak transcription	Fetal Kidney	kidney
13	chr12:58113400-58119600	Weak transcription	Hela-S3	cervix
14	chr12:58113400-58119600	Weak transcription	HSMM	muscle
15	chr12:58113400-58119600	Weak transcription	NHEK	skin
16	chr12:58113600-58116800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:58113600-58116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:58113600-58117000	Weak transcription	K562	blood
19	chr12:58113600-58119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:58113800-58117800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:58113800-58119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:58114000-58117800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:58114000-58120600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:58114200-58119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:58114400-58116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:58114400-58119000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:58114400-58119600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:58114600-58116800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:58114600-58117200	Weak transcription	Stomach Mucosa	stomach
30	chr12:58114800-58117600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:58115000-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:58115000-58119800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:58115000-58120800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:58115200-58117000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:58115200-58118000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:58115200-58118200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:58115200-58119600	Weak transcription	HUVEC	blood vessel
38	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
39	chr12:58115400-58116600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:58115400-58116800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:58115400-58118000	Weak transcription	Osteobl	bone
42	chr12:58115400-58119000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:58115400-58119600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:58115400-58119600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:58115400-58119600	Weak transcription	HepG2	liver
46	chr12:58115600-58118200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr12:58115600-58119000	Weak transcription	Primary B cells from cord blood	blood
48	chr12:58115600-58119200	Weak transcription	HMEC	breast
49	chr12:58115600-58119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:58115600-58119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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