Variant report

Variant	rs6488425
Chromosome Location	chr12:11700172-11700173
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	MAX	chr12:11699839-11700305	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr12:11699706-11700185	ECC-1	luminal epithelium:	n/a	n/a
3	ELF1	chr12:11700143-11700419	K562	blood:	n/a	n/a
4	POLR2A	chr12:11700098-11700409	K562	blood:	n/a	n/a
5	POLR2A	chr12:11699875-11700417	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:11699934-11700681	GM19193	blood:	n/a	n/a
7	TCF12	chr12:11699796-11700189	ECC-1	luminal epithelium:	n/a	n/a
8	HEY1	chr12:11699997-11700385	K562	blood:	n/a	n/a
9	POLR2A	chr12:11699874-11700644	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000247157	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]
rs10772486	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11054341	0.89[ASN][1000 genomes]
rs12582151	0.82[ASN][1000 genomes]
rs17817352	0.85[ASN][1000 genomes]
rs2416791	0.92[ASN][1000 genomes]
rs2416792	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4763703	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4763705	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6488426	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6488427	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6488428	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs74060996	0.88[ASN][1000 genomes]
rs7956437	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7960374	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7967647	0.89[ASN][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	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11696400-11700200	Enhancers	Primary hematopoietic stem cells	blood
2	chr12:11697400-11708600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:11698200-11700800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr12:11698400-11700600	Enhancers	Adipose Nuclei	Adipose
5	chr12:11698600-11700600	Enhancers	Fetal Brain Male	brain
6	chr12:11698800-11700800	Weak transcription	K562	blood
7	chr12:11699000-11700600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:11699000-11701800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:11699000-11709000	Weak transcription	Fetal Lung	lung
10	chr12:11699200-11700200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:11699200-11700200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:11699200-11700200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:11699200-11701600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:11699400-11700200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:11699400-11700200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr12:11699400-11700400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:11699400-11700600	Enhancers	Dnd41	blood
18	chr12:11699400-11700800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:11699400-11707000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:11699600-11700200	Active TSS	Stomach Smooth Muscle	stomach
21	chr12:11699600-11700600	Active TSS	Fetal Muscle Trunk	muscle
22	chr12:11699600-11701200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:11699600-11701600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:11699600-11701800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:11699600-11702600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:11699800-11700200	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr12:11699800-11700200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:11699800-11700200	Active TSS	Brain Angular Gyrus	brain
29	chr12:11699800-11700200	Active TSS	Brain Hippocampus Middle	brain
30	chr12:11699800-11700200	Flanking Active TSS	Fetal Thymus	thymus
31	chr12:11699800-11700200	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:11699800-11700400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:11699800-11700400	Active TSS	Fetal Intestine Small	intestine
34	chr12:11699800-11700600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr12:11699800-11700600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:11699800-11700600	Active TSS	Brain Anterior Caudate	brain
37	chr12:11699800-11700600	Active TSS	Brain Cingulate Gyrus	brain
38	chr12:11699800-11700600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr12:11699800-11700600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr12:11699800-11700600	Active TSS	Fetal Intestine Large	intestine
41	chr12:11699800-11700600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:11699800-11700600	Active TSS	Placenta Amnion	Placenta Amnion
43	chr12:11699800-11700600	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr12:11699800-11700800	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr12:11699800-11700800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:11699800-11700800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:11699800-11701600	Enhancers	Primary T cells from cord blood	blood
48	chr12:11700000-11700200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr12:11700000-11700200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:11700000-11700200	Enhancers	Esophagus	oesophagus

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