Variant report

Variant	rs73486829
Chromosome Location	chr13:49107841-49107842
allele	A/G
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	chr13:49105321-49107960	GM12878	blood:	n/a	n/a
2	CTCF	chr13:49107720-49107870	GM12872	blood:	n/a	n/a
3	POLR2A	chr13:49105070-49108079	GM15510	blood:	n/a	n/a
4	POLR2A	chr13:49104184-49108569	GM19099	blood:	n/a	n/a
5	MTA3	chr13:49105442-49107850	GM12878	blood:	n/a	n/a
6	HCFC1	chr13:49106021-49107892	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr13:49105979-49108447	PBDE	blood:	n/a	n/a
8	POLR2A	chr13:49104358-49108010	GM18526	blood:	n/a	n/a
9	POLR2A	chr13:49104093-49108393	GM19193	blood:	n/a	n/a
10	NRF1	chr13:49105990-49107897	SK-N-SH	brain:	n/a	chr13:49106806-49106817 chr13:49106808-49106817 chr13:49106885-49106899 chr13:49106968-49106982 chr13:49106887-49106898 chr13:49106806-49106815 chr13:49106803-49106817 chr13:49106973-49106982 chr13:49106888-49106897 chr13:49106888-49106899 chr13:49106971-49106982 chr13:49106890-49106899 chr13:49106806-49106820 chr13:49106971-49106985 chr13:49106888-49106902
11	MAZ	chr13:49106053-49108571	IMR90	lung:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
12	POLR2A	chr13:49106068-49107999	NB4	blood:	n/a	n/a
13	POLR2A	chr13:49102123-49108646	GM12891	blood:	n/a	n/a
14	POLR2A	chr13:49104148-49108484	GM18505	blood:	n/a	n/a
15	POLR2A	chr13:49103707-49108625	GM12878	blood:	n/a	n/a
16	REST	chr13:49106224-49107946	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr13:49107829-49108022	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr13:49104171-49108266	GM18951	blood:	n/a	n/a
19	POLR2A	chr13:49106041-49107935	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr13:49104669-49108203	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49107619..49110446-chr13:49111219..49113821,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RB1-2	chr13:49106976-49107897	NONHSAT033718

Variant related genes	Relation type
RCBTB2	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs4151632	1.00[AMR][1000 genomes]
rs73479233	1.00[AMR][1000 genomes]
rs73479235	1.00[AMR][1000 genomes]
rs73479241	1.00[AMR][1000 genomes]
rs73479247	1.00[AMR][1000 genomes]
rs73479252	1.00[AMR][1000 genomes]
rs73486810	1.00[AMR][1000 genomes]
rs73486817	1.00[AMR][1000 genomes]
rs73486823	1.00[AMR][1000 genomes]
rs73486824	1.00[AMR][1000 genomes]
rs73486850	1.00[AMR][1000 genomes]
rs73486858	1.00[AMR][1000 genomes]
rs73486870	1.00[AMR][1000 genomes]
rs73492996	1.00[AMR][1000 genomes]
rs73495021	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49105800-49108000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:49106000-49108000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr13:49106000-49108000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr13:49106200-49108000	Active TSS	K562	blood
5	chr13:49106200-49108400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:49107200-49108000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:49107200-49108200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr13:49107200-49108200	Flanking Active TSS	GM12878-XiMat	blood
9	chr13:49107200-49108600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr13:49107200-49110800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr13:49107400-49108000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:49107400-49108000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr13:49107400-49108000	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr13:49107400-49108200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr13:49107400-49108200	Enhancers	Stomach Mucosa	stomach
16	chr13:49107400-49108400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr13:49107600-49108000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:49107600-49108000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr13:49107600-49108000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr13:49107600-49108000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr13:49107600-49108000	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr13:49107600-49108000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:49107600-49108000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr13:49107600-49108000	Enhancers	Fetal Lung	lung
25	chr13:49107600-49108000	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr13:49107600-49108000	Flanking Active TSS	HepG2	liver
27	chr13:49107600-49108200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr13:49107600-49108200	Enhancers	Fetal Brain Male	brain
29	chr13:49107600-49108400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr13:49107600-49108400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr13:49107600-49108400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:49107600-49108400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr13:49107600-49108400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr13:49107600-49108600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr13:49107600-49108800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr13:49107800-49108000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr13:49107800-49108000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr13:49107800-49108000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr13:49107800-49108000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:49107800-49108000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr13:49107800-49108000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr13:49107800-49108000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:49107800-49108000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr13:49107800-49108000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr13:49107800-49108000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:49107800-49108000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:49107800-49108000	Enhancers	Brain Angular Gyrus	brain
48	chr13:49107800-49108000	Enhancers	Brain Germinal Matrix	brain
49	chr13:49107800-49108000	Enhancers	Brain Substantia Nigra	brain
50	chr13:49107800-49108000	Flanking Active TSS	Fetal Brain Female	brain

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