Variant report

Variant	rs12313439
Chromosome Location	chr12:42630619-42630620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:42630545-42632688	IMR90	lung:	n/a	n/a
2	HCFC1	chr12:42630358-42633508	Hela-S3	cervix:	n/a	n/a
3	MYC	chr12:42630606-42630841	MCF10A-Er-Src	breast:	n/a	n/a
4	RFX5	chr12:42630599-42630631	K562	blood:	n/a	n/a
5	CHD1	chr12:42630487-42632928	IMR90	lung:	n/a	chr12:42631292-42631302 chr12:42631852-42631862

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:42629683..42634871-chr12:42717173..42721669,10	K562	blood:
2	chr12:42629596..42634057-chr12:42635851..42641617,6	MCF-7	breast:
3	chr12:42629382..42633215-chr12:42724719..42729481,4	MCF-7	breast:
4	chr12:42630581..42632543-chr12:42717454..42720310,3	MCF-7	breast:
5	chr12:42602650..42606559-chr12:42628357..42633249,5	MCF-7	breast:
6	chr12:42536858..42540358-chr12:42630016..42633914,10	MCF-7	breast:
7	chr12:42535865..42541158-chr12:42630084..42634162,10	K562	blood:
8	chr12:42537005..42540223-chr12:42630265..42633071,6	MCF-7	breast:
9	chr12:42630585..42631302-chr8:144126589..144127131,2	MCF-7	breast:
10	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
11	chr12:42604514..42606736-chr12:42630600..42632682,2	MCF-7	breast:
12	chr12:42613730..42615825-chr12:42628835..42630747,2	K562	blood:
13	chr12:42552974..42555837-chr12:42630405..42632767,3	MCF-7	breast:

No data

Variant related genes	Relation type
PPHLN1	TF binding region
ENSG00000241710	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000139168	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11181316	1.00[AMR][1000 genomes]
rs11181323	1.00[AMR][1000 genomes]
rs11181352	1.00[AMR][1000 genomes]
rs11181358	1.00[AMR][1000 genomes]
rs11181365	1.00[AMR][1000 genomes]
rs12298117	1.00[AMR][1000 genomes]
rs12300748	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310121	1.00[AMR][1000 genomes]
rs12310800	1.00[AMR][1000 genomes]
rs12311173	1.00[AMR][1000 genomes]
rs12312552	1.00[AMR][1000 genomes]
rs12313898	1.00[AMR][1000 genomes]
rs12322282	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12322316	1.00[AMR][1000 genomes]
rs12322344	1.00[AMR][1000 genomes]
rs12322394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12385814	1.00[AMR][1000 genomes]
rs28599887	1.00[AMR][1000 genomes]
rs56736670	1.00[AMR][1000 genomes]
rs61023006	1.00[AMR][1000 genomes]
rs6582387	1.00[AMR][1000 genomes]
rs6582388	1.00[AMR][1000 genomes]
rs7306048	1.00[AMR][1000 genomes]
rs7959000	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7971397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3324521	chr12:42630510-42633558	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42569600-42630800	Weak transcription	Colonic Mucosa	Colon
2	chr12:42569800-42631000	Weak transcription	Gastric	stomach
3	chr12:42602400-42630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:42609800-42631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:42613600-42631000	Weak transcription	Ovary	ovary
6	chr12:42613800-42630800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:42620400-42630800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:42620400-42631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:42620600-42630800	Weak transcription	Fetal Intestine Small	intestine
10	chr12:42620600-42630800	Weak transcription	Fetal Stomach	stomach
11	chr12:42627200-42630800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:42628000-42631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:42628200-42631000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr12:42628600-42630800	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr12:42628600-42630800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:42628600-42630800	Enhancers	Brain Substantia Nigra	brain
17	chr12:42628600-42630800	Enhancers	Fetal Heart	heart
18	chr12:42628600-42631000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:42628600-42631000	Weak transcription	Esophagus	oesophagus
20	chr12:42628600-42631200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:42628800-42630800	Enhancers	HepG2	liver
22	chr12:42628800-42631000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:42629000-42630800	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:42629000-42631000	Enhancers	Colon Smooth Muscle	Colon
25	chr12:42629000-42631000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:42629200-42631000	Weak transcription	Stomach Mucosa	stomach
27	chr12:42629200-42633000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:42629400-42630800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:42629400-42631000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:42629400-42631000	Enhancers	Fetal Lung	lung
31	chr12:42629600-42630800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr12:42629600-42630800	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:42629600-42630800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr12:42629600-42631000	Weak transcription	Placenta	Placenta
35	chr12:42629600-42631400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:42629600-42632600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr12:42629800-42630800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:42629800-42630800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:42629800-42630800	Weak transcription	Fetal Thymus	thymus
40	chr12:42629800-42630800	Flanking Active TSS	Osteobl	bone
41	chr12:42629800-42631000	Weak transcription	Left Ventricle	heart
42	chr12:42629800-42631000	Weak transcription	Lung	lung
43	chr12:42629800-42631000	Weak transcription	Pancreas	Pancrea
44	chr12:42629800-42631000	Weak transcription	Psoas Muscle	Psoas
45	chr12:42629800-42631000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:42629800-42631000	Weak transcription	Right Ventricle	heart
47	chr12:42629800-42631000	Weak transcription	Thymus	Thymus
48	chr12:42629800-42631000	Weak transcription	Spleen	Spleen
49	chr12:42629800-42632400	Active TSS	NHLF	lung
50	chr12:42629800-42632800	Active TSS	Right Atrium	heart

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