Variant report

Variant	rs670523
Chromosome Location	chr1:155878732-155878733
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155825653..155829252-chr1:155877943..155882760,5	MCF-7	breast:
2	chr1:155868953..155871356-chr1:155876102..155879060,2	MCF-7	breast:
3	chr1:155878384..155883302-chr1:155900472..155905868,7	K562	blood:
4	chr1:155877559..155880207-chr1:155906771..155908937,2	MCF-7	breast:
5	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:

Variant related genes	Relation type
ENSG00000116580	Chromatin interaction
ENSG00000132718	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10796955	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11264422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12024880	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12027412	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12563627	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1749405	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1889532	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2993207	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3856261	0.88[JPT][hapmap]
rs4661151	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4661175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4661218	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs488079	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs490498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs539602	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs625658	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs639398	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs656247	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs656737	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs729022	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs7538214	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs821551	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap]
rs822478	1.00[ASW][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs822504	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs822505	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs822508	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[MEX][hapmap]
rs928596	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory bowel disease	23128233	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs670523	RIT1	cis	cerebellum	SCAN
rs670523	PRUNE	cis	cerebellum	SCAN
rs670523	YY1AP1	cis	cerebellum	SCAN
rs670523	SLC39A1	cis	cerebellum	SCAN
rs670523	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs670523	FAM189B	cis	cerebellum	SCAN
rs670523	SPRR3	cis	parietal	SCAN
rs670523	UBQLN4	trans	parietal	SCAN
rs670523	RIT1	cis	Thyroid	GTEx
rs670523	ROBLD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155863400-155880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155865200-155879200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:155865200-155879600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:155865600-155879200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:155865600-155879600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:155865800-155878800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:155865800-155879200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:155865800-155879400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:155865800-155879800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:155865800-155880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:155866000-155879000	Strong transcription	Liver	Liver
12	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:155866000-155879200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:155866000-155879600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:155866000-155879600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:155866000-155879600	Strong transcription	Fetal Intestine Large	intestine
18	chr1:155866000-155879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:155866000-155879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:155866000-155879800	Strong transcription	Fetal Thymus	thymus
21	chr1:155866200-155879000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:155866200-155879000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:155866200-155879800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:155866400-155879200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:155866400-155879600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:155866400-155879800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:155866800-155879000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:155867400-155879800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:155867400-155879800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:155867400-155880000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:155868400-155879400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:155868600-155879200	Strong transcription	Adipose Nuclei	Adipose
33	chr1:155868600-155879400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:155868800-155878800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:155868800-155879400	Strong transcription	Left Ventricle	heart
36	chr1:155868800-155879800	Strong transcription	Thymus	Thymus
37	chr1:155868800-155880000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr1:155869000-155879000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr1:155869000-155879800	Strong transcription	Fetal Muscle Leg	muscle
40	chr1:155869000-155879800	Strong transcription	Fetal Stomach	stomach
41	chr1:155869200-155879800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:155869800-155879600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:155870200-155879200	Strong transcription	Fetal Intestine Small	intestine
44	chr1:155870600-155879000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:155870600-155879000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:155873000-155879200	Strong transcription	Osteobl	bone
47	chr1:155873200-155879200	Strong transcription	HUVEC	blood vessel
48	chr1:155873200-155879400	Strong transcription	NHDF-Ad	bronchial
49	chr1:155873200-155879800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:155873400-155879200	Strong transcription	NH-A	brain

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