Variant report

Variant	rs12124649
Chromosome Location	chr1:46499207-46499208
allele	A/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	chr1:46499058-46504138	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:46499085-46500199	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:46499138-46500223	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:46499135-46503774	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46496781..46499217-chr1:46640648..46642564,2	K562	blood:
2	chr1:46498806..46500907-chr1:46597285..46600123,2	MCF-7	breast:
3	chr1:46498325..46500159-chr1:46595927..46599001,3	K562	blood:
4	chr1:46495760..46499404-chr1:46501029..46505549,6	K562	blood:

Variant related genes	Relation type
MAST2	TF binding region
ENSG00000250719	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12116773	0.80[EUR][1000 genomes]
rs12120708	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12141934	1.00[CEU][hapmap]
rs12142296	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12143448	1.00[CEU][hapmap]
rs12143773	0.89[EUR][1000 genomes]
rs12143865	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17102061	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009527	chr1:46286329-46520127	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv829737	chr1:46352900-46506424	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv522438	chr1:46462881-46500993	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	esv1795204	chr1:46466373-46504466	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
15	esv1829371	chr1:46466373-46504466	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	nsv1007750	chr1:46471293-46552564	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
17	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
18	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
19	nsv515934	chr1:46493460-46502836	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12124649	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12124649	IPP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46473000-46500400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:46473600-46502600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:46474400-46502600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:46475600-46525000	Weak transcription	Fetal Kidney	kidney
5	chr1:46476200-46502600	Weak transcription	Stomach Mucosa	stomach
6	chr1:46476600-46515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:46484800-46502000	Strong transcription	Fetal Intestine Small	intestine
8	chr1:46485000-46502000	Strong transcription	Fetal Stomach	stomach
9	chr1:46485800-46503000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:46486800-46502400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:46487000-46502000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:46487200-46500800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr1:46487200-46501600	Strong transcription	Fetal Brain Female	brain
14	chr1:46487600-46501600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:46488800-46501800	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:46488800-46505200	Weak transcription	HMEC	breast
17	chr1:46490200-46524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:46490600-46505000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:46490600-46525200	Weak transcription	NH-A	brain
20	chr1:46492000-46507600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:46492200-46501400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:46492600-46500400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:46492600-46502000	Strong transcription	Fetal Intestine Large	intestine
24	chr1:46492800-46501200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:46492800-46502000	Strong transcription	Brain Germinal Matrix	brain
26	chr1:46493000-46501200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:46493000-46501600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:46493000-46502400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:46493000-46509200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:46493200-46500200	Strong transcription	Brain Substantia Nigra	brain
31	chr1:46493200-46501000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:46493200-46501000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:46493200-46501200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:46493200-46501200	Strong transcription	Colonic Mucosa	Colon
35	chr1:46493200-46501400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:46493200-46501800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:46493200-46502200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:46493400-46500200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:46493400-46500800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:46493400-46501200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:46493400-46501400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:46493400-46501400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:46493400-46501400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:46493400-46502000	Strong transcription	Placenta	Placenta
45	chr1:46493600-46500400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:46493600-46500800	Strong transcription	Adipose Nuclei	Adipose
47	chr1:46493600-46500800	Strong transcription	Liver	Liver
48	chr1:46493600-46501400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:46493600-46501400	Strong transcription	Lung	lung
50	chr1:46493600-46501400	Strong transcription	Dnd41	blood

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