Variant report

Variant	rs59666900
Chromosome Location	chr5:179147641-179147642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179147476-179148520	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179144485..179148247-chr5:179156988..179160765,4	K562	blood:
2	chr5:179143486..179153989-chr5:179156108..179164461,19	MCF-7	breast:
3	chr5:179126981..179129032-chr5:179147210..179150124,2	K562	blood:
4	chr5:179146141..179147702-chr5:179190620..179192713,2	MCF-7	breast:
5	chr5:179104984..179107409-chr5:179146217..179147861,2	K562	blood:
6	chr5:179147273..179149282-chr5:179155008..179157587,2	MCF-7	breast:

No data

Variant related genes	Relation type
CANX	TF binding region
ENSG00000161021	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12656648	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34646062	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55882075	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62404346	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6867806	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7732112	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59666900	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179127800-179152000	Strong transcription	NHEK	skin
2	chr5:179127800-179156400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:179127800-179156600	Strong transcription	Fetal Stomach	stomach
4	chr5:179127800-179158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:179128200-179156400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:179128400-179157800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:179128400-179157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:179128400-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:179128400-179159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:179128600-179150400	Weak transcription	Stomach Mucosa	stomach
11	chr5:179128600-179158200	Strong transcription	Fetal Muscle Leg	muscle
12	chr5:179129000-179158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:179129200-179157600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr5:179129400-179152600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:179129400-179158200	Strong transcription	Fetal Thymus	thymus
16	chr5:179129600-179157400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:179129800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:179129800-179158200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:179129800-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:179129800-179158200	Strong transcription	Fetal Intestine Large	intestine
21	chr5:179129800-179158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:179130400-179158200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:179130600-179157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:179130600-179157600	Strong transcription	HUVEC	blood vessel
25	chr5:179130800-179156400	Strong transcription	Liver	Liver
26	chr5:179130800-179158200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:179130800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:179130800-179159800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:179131000-179157600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr5:179131000-179157800	Strong transcription	Dnd41	blood
31	chr5:179131000-179158200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:179131200-179154200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:179131200-179158000	Strong transcription	Placenta	Placenta
34	chr5:179132000-179158200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr5:179132200-179152200	Strong transcription	HSMM	muscle
36	chr5:179132200-179152600	Strong transcription	NH-A	brain
37	chr5:179132400-179152600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:179132400-179152600	Strong transcription	A549	lung
39	chr5:179132400-179152600	Strong transcription	HMEC	breast
40	chr5:179132400-179157400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:179132400-179157400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:179132800-179156600	Strong transcription	Lung	lung
43	chr5:179132800-179158200	Strong transcription	Adipose Nuclei	Adipose
44	chr5:179132800-179158200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr5:179133000-179154800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:179133000-179158000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:179133000-179158200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:179133000-179158200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:179133000-179158200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:179133000-179158200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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