Variant report

Variant	rs12829179
Chromosome Location	chr12:51719989-51719990
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51716760-51720317	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51475890..51478856-chr12:51719210..51722345,3	K562	blood:
2	chr12:51632967..51634708-chr12:51718961..51721755,2	K562	blood:
3	chr12:51417902..51420501-chr12:51719275..51722211,2	K562	blood:
4	chr12:51156096..51157796-chr12:51717451..51720427,2	MCF-7	breast:
5	chr12:51663552..51665090-chr12:51718894..51721818,2	MCF-7	breast:
6	chr12:51719185..51720763-chr12:51721819..51723856,2	MCF-7	breast:
7	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
8	chr12:51712710..51716828-chr12:51719754..51724043,5	K562	blood:
9	chr12:51633168..51635077-chr12:51718759..51720463,2	MCF-7	breast:

No data

Variant related genes	Relation type
BIN2	TF binding region
ENSG00000110925	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10516	0.93[EUR][1000 genomes]
rs10876162	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169805	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11616158	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310910	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12582273	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12830766	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12831721	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860300	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860301	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860343	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858624	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3858627	0.82[EUR][1000 genomes]
rs57941347	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61022955	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68042460	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7133606	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7138439	0.88[EUR][1000 genomes]
rs7299306	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7299453	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7306746	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7959814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964134	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9651999	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51711800-51721800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:51712800-51720200	Weak transcription	HMEC	breast
3	chr12:51713200-51720000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:51715000-51720000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:51715000-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:51715000-51720000	Weak transcription	Hela-S3	cervix
7	chr12:51715000-51720000	Weak transcription	HSMM	muscle
8	chr12:51715000-51720200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:51715000-51720200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:51715000-51720200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:51715200-51720000	Weak transcription	HSMMtube	muscle
12	chr12:51715200-51720200	Weak transcription	NHDF-Ad	bronchial
13	chr12:51715200-51720400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:51715200-51720600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:51715600-51720200	Weak transcription	A549	lung
16	chr12:51715600-51720800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:51715800-51720200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:51715800-51720400	Weak transcription	Fetal Lung	lung
19	chr12:51715800-51720400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:51715800-51720600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:51716000-51720600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:51717600-51721000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:51717600-51722600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:51717800-51720000	Weak transcription	Liver	Liver
25	chr12:51717800-51720000	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:51717800-51720000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:51717800-51720400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:51717800-51722200	Weak transcription	Small Intestine	intestine
29	chr12:51718000-51720200	Weak transcription	Right Atrium	heart
30	chr12:51718000-51720400	Enhancers	Spleen	Spleen
31	chr12:51718000-51722400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
33	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:51718200-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:51718200-51720200	Enhancers	K562	blood
36	chr12:51718200-51720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:51718400-51720200	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:51718400-51720200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:51718400-51720400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:51718400-51720400	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:51718400-51720400	Enhancers	GM12878-XiMat	blood
42	chr12:51718400-51720600	Enhancers	Primary B cells from cord blood	blood
43	chr12:51718400-51720600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr12:51718400-51721200	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:51718400-51722200	Enhancers	Primary T cells from cord blood	blood
46	chr12:51718400-51722400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:51718400-51722400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:51718400-51722600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr12:51718400-51723000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:51718400-51723200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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