Variant report

Variant	rs1677129
Chromosome Location	chr12:21791565-21791566
allele	G/T
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	MAFF	chr12:21791486-21791772	K562	blood:	n/a	n/a
2	EP300	chr12:21791274-21791763	A549	lung:	n/a	chr12:21791415-21791429 chr12:21791645-21791652 chr12:21791411-21791425
3	STAT3	chr12:21791444-21791615	MCF10A-Er-Src	breast:	n/a	n/a
4	MAFK	chr12:21791450-21791779	IMR90	lung:	n/a	chr12:21791642-21791652
5	MAFK	chr12:21791520-21791749	HepG2	liver:	n/a	chr12:21791642-21791652
6	EP300	chr12:21791540-21791590	K562	blood:	n/a	n/a
7	JUND	chr12:21791532-21791705	K562	blood:	n/a	n/a
8	GATA1	chr12:21790753-21791929	PBDE	blood:	n/a	chr12:21791143-21791159 chr12:21791156-21791177
9	MAFK	chr12:21791479-21791786	K562	blood:	n/a	chr12:21791642-21791652
10	POLR2A	chr12:21791541-21791751	K562	blood:	n/a	n/a
11	POLR2A	chr12:21791307-21791765	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LDHB	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10841863	0.87[AFR][1000 genomes]
rs10841864	0.87[AFR][1000 genomes]
rs10841865	0.87[AFR][1000 genomes]
rs10841866	0.87[AFR][1000 genomes]
rs11836605	1.00[AMR][1000 genomes]
rs1283818	1.00[AMR][1000 genomes]
rs153942	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1624003	0.87[AFR][1000 genomes]
rs1626167	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1626303	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1630514	0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs1650272	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1650277	0.86[ASW][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1650278	0.87[AFR][1000 genomes]
rs1650279	0.87[AFR][1000 genomes]
rs1650280	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1650283	0.94[AFR][1000 genomes]
rs1650285	0.87[AFR][1000 genomes]
rs1650288	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs1650294	0.86[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1650311	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677075	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs1677080	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677088	0.87[AFR][1000 genomes]
rs1677090	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677092	0.87[AFR][1000 genomes]
rs1677093	0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs1677094	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1677095	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1677096	0.87[AFR][1000 genomes]
rs1677097	0.87[AFR][1000 genomes]
rs1677098	0.87[AFR][1000 genomes]
rs1677100	0.87[AFR][1000 genomes]
rs1677113	1.00[AFR][1000 genomes]
rs1677118	0.86[AFR][1000 genomes]
rs1677124	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677128	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1677134	1.00[ASW][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677135	0.87[AFR][1000 genomes]
rs1677136	0.87[AFR][1000 genomes]
rs1677139	0.87[AFR][1000 genomes]
rs1677140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677141	0.86[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs255445	0.87[AFR][1000 genomes]
rs255450	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs255452	0.86[AFR][1000 genomes]
rs255454	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2559823	0.82[AFR][1000 genomes]
rs2617118	0.86[AFR][1000 genomes]
rs4438091	0.84[AFR][1000 genomes]
rs4762714	0.87[AFR][1000 genomes]
rs4762856	0.87[AFR][1000 genomes]
rs4762858	0.87[AFR][1000 genomes]
rs4762859	0.87[AFR][1000 genomes]
rs4762862	0.87[AFR][1000 genomes]
rs60507695	1.00[AMR][1000 genomes]
rs60867568	1.00[AMR][1000 genomes]
rs61320912	1.00[AMR][1000 genomes]
rs7299674	0.84[AFR][1000 genomes]
rs7299680	0.87[AFR][1000 genomes]
rs7300051	0.87[AFR][1000 genomes]
rs73249205	1.00[AMR][1000 genomes]
rs73258133	1.00[AMR][1000 genomes]
rs73260142	1.00[AMR][1000 genomes]
rs73260149	1.00[AMR][1000 genomes]
rs73262354	1.00[AMR][1000 genomes]
rs73262383	1.00[AMR][1000 genomes]
rs73262391	1.00[AMR][1000 genomes]
rs73262395	1.00[AMR][1000 genomes]
rs73266378	1.00[AMR][1000 genomes]
rs73266381	1.00[AMR][1000 genomes]
rs759933	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974267	0.87[AFR][1000 genomes]
rs829071	1.00[AMR][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	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv469164	chr12:21688900-21966701	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv557744	chr12:21688900-21966701	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv832349	chr12:21749093-21930695	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21781200-21796400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:21781200-21809600	Weak transcription	Small Intestine	intestine
3	chr12:21782600-21805400	Weak transcription	Colonic Mucosa	Colon
4	chr12:21783800-21801600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:21784600-21792400	Strong transcription	Fetal Thymus	thymus
6	chr12:21785000-21801400	Strong transcription	Dnd41	blood
7	chr12:21785200-21793600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:21785200-21798600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:21785400-21793600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:21785400-21797600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:21785400-21805200	Strong transcription	GM12878-XiMat	blood
12	chr12:21785600-21794800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:21785800-21797000	Strong transcription	Primary B cells from cord blood	blood
14	chr12:21785800-21797200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:21785800-21807600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:21786000-21793600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:21786000-21793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:21786000-21796200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:21786200-21791800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:21786200-21792000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:21786200-21797600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:21786200-21807000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:21786400-21795600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:21786400-21796600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:21786400-21807800	Strong transcription	Osteobl	bone
26	chr12:21786600-21792200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:21786800-21791800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:21786800-21799200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:21786800-21805000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:21786800-21807400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:21787000-21795600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:21787000-21801400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:21787000-21807000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:21787000-21807800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:21787000-21807800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr12:21787200-21791800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr12:21787200-21792200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:21787200-21792200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr12:21787200-21793800	Strong transcription	NHLF	lung
40	chr12:21787200-21796000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:21787200-21796200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:21787200-21796200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:21787200-21796200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:21787200-21798400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:21787200-21806800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr12:21787200-21807400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr12:21787200-21807600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:21787200-21808200	Strong transcription	NH-A	brain
49	chr12:21787200-21808600	Strong transcription	HMEC	breast
50	chr12:21787200-21808600	Strong transcription	HSMM	muscle

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