Variant report

Variant	rs639398
Chromosome Location	chr1:155890238-155890239
allele	A/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	chr1:155890137-155891497	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:155890234-155891858	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:155890206-155891516	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:155890156-155890721	K562	blood:	n/a	n/a
5	POLR2A	chr1:155890134-155891462	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:155889675-155892623	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155889116..155891316-chr1:155948021..155950216,2	K562	blood:

Variant related genes	Relation type
KIAA0907	TF binding region
SNORA42	TF binding region
ENSG00000273002	Chromatin interaction
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11264422	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12024880	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12027412	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563627	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1749405	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2993207	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4661151	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4661175	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs488079	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs490498	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs539602	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs625658	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656247	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs656737	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs670523	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7538214	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs822504	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs639398	RIT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155881400-155890400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:155881600-155890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:155881800-155893600	Strong transcription	HMEC	breast
4	chr1:155881800-155898800	Strong transcription	HUVEC	blood vessel
5	chr1:155881800-155899800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:155881800-155900600	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:155881800-155901200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:155881800-155901200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:155882000-155898800	Strong transcription	NH-A	brain
10	chr1:155882000-155899400	Strong transcription	Fetal Intestine Large	intestine
11	chr1:155882000-155899800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:155882000-155900000	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:155882000-155900000	Strong transcription	Liver	Liver
14	chr1:155882000-155900200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:155882000-155900400	Strong transcription	Primary B cells from cord blood	blood
16	chr1:155882000-155900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:155882000-155900600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:155882000-155900600	Strong transcription	Placenta	Placenta
19	chr1:155882000-155900600	Strong transcription	Fetal Stomach	stomach
20	chr1:155882000-155900600	Strong transcription	Left Ventricle	heart
21	chr1:155882000-155900800	Strong transcription	Thymus	Thymus
22	chr1:155882000-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:155882000-155901400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:155882000-155901400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:155882200-155898600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:155882200-155900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:155882200-155900600	Strong transcription	Fetal Thymus	thymus
28	chr1:155882200-155901000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:155882200-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:155882200-155901200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:155882200-155901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:155882200-155901400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:155882200-155901400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:155882200-155903000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:155882400-155893800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:155882400-155898800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:155882400-155900000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:155882400-155900000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:155882400-155900000	Strong transcription	Adipose Nuclei	Adipose
40	chr1:155882400-155900200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:155882600-155898800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:155882600-155899000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:155882600-155899000	Strong transcription	NHEK	skin
44	chr1:155882600-155900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:155882600-155900200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:155882600-155901600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:155882600-155901600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:155882800-155897400	Strong transcription	Fetal Brain Female	brain
49	chr1:155882800-155897400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:155882800-155897800	Strong transcription	A549	lung

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