Variant report

Variant	rs10903245
Chromosome Location	chr5:179133608-179133609
allele	C/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	POLR2A	chr5:179133324-179133893	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179048674..179050755-chr5:179131427..179133888,2	MCF-7	breast:
2	chr5:179130512..179134437-chr5:179159497..179161438,3	MCF-7	breast:
3	chr5:179123586..179129079-chr5:179129217..179136579,19	MCF-7	breast:
4	chr5:179131963..179134145-chr5:179158329..179159855,2	K562	blood:

Variant related genes	Relation type
CANX	TF binding region
ENSG00000127022	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10447303	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10447304	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10516146	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10794700	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744662	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374446	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522926	0.83[AMR][1000 genomes]
rs13172893	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13174472	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13182141	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13184690	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34329357	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34785307	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35320050	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797774	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56227602	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56807514	0.90[EUR][1000 genomes]
rs62404348	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406180	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601073	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7444571	0.83[ASN][1000 genomes]
rs7732112	0.83[AFR][1000 genomes]
rs7736300	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[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
rs10903245	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179127400-179137800	Weak transcription	Aorta	Aorta
2	chr5:179127800-179133800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:179127800-179133800	Weak transcription	Colonic Mucosa	Colon
4	chr5:179127800-179134000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:179127800-179134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:179127800-179136000	Weak transcription	HSMMtube	muscle
7	chr5:179127800-179152000	Strong transcription	NHEK	skin
8	chr5:179127800-179156400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:179127800-179156600	Strong transcription	Fetal Stomach	stomach
10	chr5:179127800-179158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:179128000-179135000	Weak transcription	Esophagus	oesophagus
12	chr5:179128200-179156400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:179128400-179143200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:179128400-179157800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:179128400-179157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:179128400-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:179128400-179159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:179128600-179150400	Weak transcription	Stomach Mucosa	stomach
19	chr5:179128600-179158200	Strong transcription	Fetal Muscle Leg	muscle
20	chr5:179129000-179158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:179129200-179133800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:179129200-179146800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:179129200-179157600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr5:179129400-179134800	Weak transcription	Ovary	ovary
25	chr5:179129400-179136600	Weak transcription	Small Intestine	intestine
26	chr5:179129400-179141400	Strong transcription	Hela-S3	cervix
27	chr5:179129400-179143200	Weak transcription	Fetal Brain Male	brain
28	chr5:179129400-179152600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:179129400-179158200	Strong transcription	Fetal Thymus	thymus
30	chr5:179129600-179157400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:179129800-179135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:179129800-179143000	Weak transcription	Fetal Heart	heart
33	chr5:179129800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:179129800-179158200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:179129800-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:179129800-179158200	Strong transcription	Fetal Intestine Large	intestine
37	chr5:179129800-179158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:179130000-179136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:179130200-179138600	Strong transcription	Fetal Lung	lung
40	chr5:179130400-179137000	Weak transcription	Psoas Muscle	Psoas
41	chr5:179130400-179158200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:179130600-179157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:179130600-179157600	Strong transcription	HUVEC	blood vessel
44	chr5:179130800-179156400	Strong transcription	Liver	Liver
45	chr5:179130800-179158200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr5:179130800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:179130800-179159800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:179131000-179133800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:179131000-179133800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:179131000-179136000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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