Variant report

Variant	rs6416298
Chromosome Location	chr12:123002143-123002144
allele	C/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	POLR2A	chr12:122999444-123002873	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123002113-123002917	GM12878	blood:	n/a	n/a
3	MXI1	chr12:123002074-123002954	IMR90	lung:	n/a	n/a
4	POLR2A	chr12:123002096-123002913	U87	brain:	n/a	n/a
5	POLR2A	chr12:123002096-123002895	U87	brain:	n/a	n/a

Variant related genes	Relation type
RSRC2	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10734924	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10744275	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10773208	0.84[EUR][1000 genomes]
rs10773302	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10846978	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10847179	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10998	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11058402	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1392236	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1473553	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2062506	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2173628	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2342082	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803005	0.81[AMR][1000 genomes]
rs4319547	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6489071	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6489157	0.81[AMR][1000 genomes]
rs6489159	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7295397	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7301515	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7307735	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7314638	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7316149	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7955203	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7966094	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7972728	0.81[EUR][1000 genomes]
rs9705654	0.81[EUR][1000 genomes]
rs9988963	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122986200-123007600	Weak transcription	Right Atrium	heart
2	chr12:122986400-123003200	Strong transcription	Fetal Stomach	stomach
3	chr12:122986400-123007800	Strong transcription	Placenta	Placenta
4	chr12:122986800-123006600	Strong transcription	Brain Germinal Matrix	brain
5	chr12:122986800-123006800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:122986800-123007000	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:122986800-123009400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:122987000-123007800	Strong transcription	Fetal Thymus	thymus
9	chr12:122987200-123003200	Strong transcription	Fetal Intestine Small	intestine
10	chr12:122987400-123003000	Strong transcription	Lung	lung
11	chr12:122987400-123006800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr12:122987400-123007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:122987400-123007200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:122987400-123007400	Strong transcription	Thymus	Thymus
15	chr12:122987400-123007600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:122987400-123007800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:122987400-123007800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:122987600-123002200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:122987600-123002600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:122987600-123003600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:122987600-123004000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:122987600-123004600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:122987600-123006000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:122987600-123006400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:122987600-123006400	Strong transcription	Liver	Liver
26	chr12:122987600-123006400	Strong transcription	Brain Hippocampus Middle	brain
27	chr12:122987600-123006600	Strong transcription	Primary T cells from cord blood	blood
28	chr12:122987600-123006800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:122987600-123007000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:122987600-123007000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:122987600-123007000	Strong transcription	Fetal Intestine Large	intestine
32	chr12:122987600-123007000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:122987600-123007600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:122987600-123007600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:122987600-123008000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:122987800-123002600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:122987800-123002600	Strong transcription	Dnd41	blood
38	chr12:122987800-123002600	Strong transcription	NHDF-Ad	bronchial
39	chr12:122987800-123003200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:122987800-123003400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:122987800-123003400	Strong transcription	Spleen	Spleen
42	chr12:122987800-123004000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:122987800-123004200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:122987800-123004600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:122987800-123004600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:122987800-123005600	Strong transcription	Pancreas	Pancrea
47	chr12:122987800-123005600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:122987800-123006400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:122987800-123006400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr12:122987800-123006400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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