Variant report

Variant	rs7541060
Chromosome Location	chr1:155728088-155728089
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	CEBPB	chr1:155727996-155728246	HepG2	liver:	n/a	chr1:155728089-155728102 chr1:155728089-155728100 chr1:155728090-155728101
2	CEBPB	chr1:155728077-155728119	A549	lung:	n/a	chr1:155728089-155728102 chr1:155728089-155728100 chr1:155728090-155728101

Variant related genes	Relation type
GON4L	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10908471	0.92[JPT][hapmap]
rs10908479	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10908480	0.84[ASN][1000 genomes]
rs10908481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10908482	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264409	0.97[ASN][1000 genomes]
rs11264410	0.91[ASN][1000 genomes]
rs12035524	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12040894	0.88[ASN][1000 genomes]
rs12047756	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12081192	0.86[ASN][1000 genomes]
rs12407800	0.83[ASN][1000 genomes]
rs12744132	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1556488	0.81[JPT][hapmap]
rs2048431	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2175391	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2297775	0.94[ASN][1000 genomes]
rs2666826	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs28582361	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28662267	0.91[ASN][1000 genomes]
rs2948071	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2948072	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2985707	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs348196	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3738590	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3820594	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs3892792	0.92[JPT][hapmap]
rs4278368	0.98[ASN][1000 genomes]
rs475550	1.00[JPT][hapmap]
rs490608	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427286	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644853	0.84[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs6662953	0.86[ASN][1000 genomes]
rs6665227	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs670876	0.86[CHB][hapmap]
rs678157	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs708611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs729022	0.81[CEU][hapmap]
rs7521594	0.81[ASN][1000 genomes]
rs7550402	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821551	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs822025	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs822478	0.90[CHB][hapmap]
rs822490	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs822505	0.81[CEU][hapmap]
rs822508	0.81[CEU][hapmap]
rs822527	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9426933	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	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
3	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7541060	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	chr1:155715400-155730000	Weak transcription	Stomach Mucosa	stomach
2	chr1:155715400-155739200	Weak transcription	Fetal Heart	heart
3	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:155717200-155761000	Strong transcription	Fetal Stomach	stomach
8	chr1:155717400-155731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:155717400-155733400	Strong transcription	Brain Anterior Caudate	brain
10	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:155717600-155733800	Strong transcription	Spleen	Spleen
12	chr1:155717600-155750200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:155718000-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:155718200-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:155720000-155732000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:155720200-155732800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:155720200-155732800	Strong transcription	Osteobl	bone
18	chr1:155720200-155733000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:155720200-155733800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:155720200-155745400	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:155720200-155748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:155720200-155748800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:155720200-155748800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:155720200-155749000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:155720200-155749600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:155720200-155750200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:155720200-155750600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:155720200-155755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:155720200-155756200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:155720200-155756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
32	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:155720400-155730400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:155720400-155731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:155720400-155732600	Strong transcription	HSMM	muscle
36	chr1:155720400-155732800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:155720400-155732800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:155720400-155733000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:155720400-155733000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:155720400-155733800	Strong transcription	Left Ventricle	heart
41	chr1:155720400-155743200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:155720400-155743200	Strong transcription	Thymus	Thymus
43	chr1:155720400-155750200	Strong transcription	Adipose Nuclei	Adipose
44	chr1:155720400-155750400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:155720400-155750600	Strong transcription	Dnd41	blood
46	chr1:155720400-155755600	Strong transcription	Placenta	Placenta
47	chr1:155720400-155756400	Strong transcription	Liver	Liver
48	chr1:155720400-155760800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:155720400-155796800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:155720600-155732200	Strong transcription	Muscle Satellite Cultured Cells	--

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