Variant report

Variant	rs34484573
Chromosome Location	chr3:49880399-49880400
allele	A/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	REST	chr3:49880193-49880531	SK-N-SH	brain:	n/a	chr3:49880363-49880383 chr3:49880411-49880424 chr3:49880364-49880382
2	CTCF	chr3:49880300-49880450	GM12875	blood:	n/a	n/a
3	USF1	chr3:49880301-49880991	H1-hESC	embryonic stem cell:	n/a	chr3:49880518-49880529
4	USF1	chr3:49880311-49880626	H1-hESC	embryonic stem cell:	n/a	chr3:49880518-49880529

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49709674..49711782-chr3:49878880..49881379,2	K562	blood:

Variant related genes	Relation type
TRAIP	TF binding region
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs35441946	1.00[ASN][1000 genomes]
rs35917071	1.00[ASN][1000 genomes]
rs4395393	1.00[ASN][1000 genomes]
rs67070774	1.00[ASN][1000 genomes]
rs71325001	1.00[ASN][1000 genomes]
rs73074855	1.00[ASN][1000 genomes]
rs73077107	1.00[ASN][1000 genomes]
rs73077157	1.00[ASN][1000 genomes]
rs73079003	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079014	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34484573	IHPK2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
5	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
6	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:49864600-49882000	Weak transcription	Osteobl	bone
8	chr3:49864800-49880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:49865000-49886000	Strong transcription	Dnd41	blood
11	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:49866000-49881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:49869000-49883200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:49869200-49881000	Weak transcription	HMEC	breast
16	chr3:49869400-49880400	Weak transcription	Spleen	Spleen
17	chr3:49869400-49893000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:49870200-49893000	Weak transcription	HSMM	muscle
19	chr3:49871200-49886000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:49873600-49885800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49873800-49885800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:49874000-49885800	Strong transcription	Thymus	Thymus
23	chr3:49874800-49882000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:49876000-49880600	Weak transcription	NHEK	skin
25	chr3:49876000-49880800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:49876000-49881800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49876000-49882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:49876200-49880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:49876600-49881200	Enhancers	Fetal Heart	heart
30	chr3:49877000-49882400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:49877000-49893000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:49877000-49893400	Weak transcription	HSMMtube	muscle
33	chr3:49877200-49880600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:49877200-49880600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:49877200-49882200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:49877200-49885000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:49877200-49886000	Weak transcription	Stomach Mucosa	stomach
38	chr3:49877200-49893000	Weak transcription	Gastric	stomach
39	chr3:49877200-49893000	Weak transcription	NHDF-Ad	bronchial
40	chr3:49877200-49893200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:49877400-49881800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:49877400-49882600	Weak transcription	Ovary	ovary
43	chr3:49877400-49883000	Weak transcription	Liver	Liver
44	chr3:49877400-49883000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:49877400-49893000	Weak transcription	A549	lung
46	chr3:49877400-49893200	Weak transcription	Lung	lung
47	chr3:49877400-49893200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:49877600-49893200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:49877800-49885800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:49877800-49893000	Weak transcription	Esophagus	oesophagus

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