Variant report

Variant	rs2993207
Chromosome Location	chr1:155873314-155873315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155862010..155864371-chr1:155873312..155876072,2	MCF-7	breast:
2	chr1:155867375..155873348-chr1:155878269..155881617,9	K562	blood:

Variant related genes	Relation type
ENSG00000143622	Chromatin interaction
ENSG00000201614	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10796955	0.80[CHB][hapmap]
rs11264422	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12024880	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12027412	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12563627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1749410	0.88[ASN][1000 genomes]
rs1889532	0.80[CHB][hapmap]
rs3820594	0.80[JPT][hapmap]
rs4661151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4661175	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4661218	0.80[CHB][hapmap]
rs488079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs490498	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs539602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639398	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs656247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs656737	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs670523	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]
rs729022	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7517204	0.88[ASN][1000 genomes]
rs7538214	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs822490	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs822504	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs822505	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs822508	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.88[ASN][1000 genomes]
rs822509	0.88[ASN][1000 genomes]
rs860295	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs928596	0.80[CHB][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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2993207	YY1AP1	cis	cerebellum	SCAN
rs2993207	FAM189B	cis	cerebellum	SCAN
rs2993207	SPRR3	cis	parietal	SCAN
rs2993207	PRUNE	cis	cerebellum	SCAN
rs2993207	ROBLD3	cis	parietal	SCAN
rs2993207	RIT1	cis	cerebellum	SCAN
rs2993207	SLC39A1	cis	cerebellum	SCAN
rs2993207	UBQLN4	trans	parietal	SCAN
rs2993207	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	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
2	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155862800-155873600	Weak transcription	Psoas Muscle	Psoas
5	chr1:155863400-155873600	Weak transcription	Stomach Mucosa	stomach
6	chr1:155863400-155880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:155863800-155874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:155865000-155875400	Strong transcription	Fetal Brain Female	brain
9	chr1:155865200-155878600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:155865200-155879200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:155865200-155879600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155865400-155873600	Strong transcription	Placenta	Placenta
13	chr1:155865600-155879200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:155865600-155879600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:155865800-155878400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:155865800-155878800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:155865800-155879200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:155865800-155879400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:155865800-155879800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:155865800-155880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:155866000-155879000	Strong transcription	Liver	Liver
22	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:155866000-155879200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:155866000-155879600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:155866000-155879600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:155866000-155879600	Strong transcription	Fetal Intestine Large	intestine
28	chr1:155866000-155879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:155866000-155879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:155866000-155879800	Strong transcription	Fetal Thymus	thymus
31	chr1:155866200-155875400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:155866200-155879000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:155866200-155879000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:155866200-155879800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:155866400-155875400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:155866400-155877600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:155866400-155878000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:155866400-155879200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:155866400-155879600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:155866400-155879800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:155866600-155875400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:155866600-155878400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:155866800-155879000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:155867000-155873400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:155867400-155878600	Strong transcription	Dnd41	blood
46	chr1:155867400-155879800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:155867400-155879800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:155867400-155880000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:155868400-155875200	Strong transcription	Brain Germinal Matrix	brain
50	chr1:155868400-155877600	Strong transcription	Rectal Mucosa Donor 31	rectum

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