Variant report

Variant	rs59384609
Chromosome Location	chr12:123834544-123834545
allele	C/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	chr12:123834489-123834740	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123832815..123836496-chr12:123847723..123851604,4	MCF-7	breast:
2	chr12:123833002..123837136-chr12:123847313..123849620,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207189	TF binding region
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs59799766	0.91[AFR][1000 genomes]
rs73421388	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7980481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123773000-123835200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:123773200-123835000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:123773200-123835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:123773200-123838000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:123773400-123835000	Strong transcription	Fetal Thymus	thymus
7	chr12:123773400-123835400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:123773400-123837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:123773600-123835200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:123773600-123835400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:123773800-123834800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr12:123773800-123837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:123773800-123837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:123774000-123835000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:123774000-123835200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:123774000-123835400	Strong transcription	Dnd41	blood
17	chr12:123775600-123835400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:123776400-123835000	Strong transcription	Thymus	Thymus
19	chr12:123777000-123835400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:123777600-123834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123785600-123835000	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:123790200-123835000	Strong transcription	Fetal Intestine Large	intestine
23	chr12:123805200-123835200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:123807600-123845200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:123812200-123835200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:123813800-123835600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:123815200-123835600	Strong transcription	Fetal Intestine Small	intestine
28	chr12:123815200-123837200	Strong transcription	Fetal Stomach	stomach
29	chr12:123815400-123835000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:123815600-123842000	Weak transcription	Psoas Muscle	Psoas
31	chr12:123816000-123838400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:123816000-123847400	Weak transcription	Stomach Mucosa	stomach
33	chr12:123817800-123834800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:123820400-123847000	Weak transcription	Fetal Brain Male	brain
35	chr12:123821600-123835600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr12:123823600-123835000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:123825800-123835000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:123826600-123835000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:123826800-123834800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:123826800-123835000	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr12:123827000-123834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:123827000-123835000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:123827200-123835000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr12:123827200-123835000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:123827400-123835000	Strong transcription	Fetal Lung	lung
46	chr12:123827800-123835000	Strong transcription	Brain Germinal Matrix	brain
47	chr12:123827800-123835600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:123829000-123839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:123829000-123847400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:123829400-123840200	Weak transcription	Ovary	ovary

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