Variant report

Variant	rs4661151
Chromosome Location	chr1:155903408-155903409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155893064..155900339-chr1:155902644..155906758,10	MCF-7	breast:
2	chr1:155884685..155887333-chr1:155903163..155905459,3	MCF-7	breast:
3	chr1:155902449..155905054-chr1:155910368..155915421,5	MCF-7	breast:
4	chr1:155902752..155906488-chr1:155946119..155948945,5	MCF-7	breast:
5	chr1:155902819..155904971-chr1:156082922..156085849,2	K562	blood:
6	chr1:155901303..155903667-chr1:156040998..156043526,2	K562	blood:
7	chr1:155902248..155903892-chr1:155972223..155974691,2	K562	blood:
8	chr1:155824896..155829386-chr1:155902844..155905236,4	MCF-7	breast:
9	chr1:155902986..155905727-chr1:155989614..155992044,2	MCF-7	breast:
10	chr1:155902774..155905937-chr1:155970220..155974829,6	K562	blood:
11	chr1:155902649..155906864-chr1:155928278..155934368,7	MCF-7	breast:
12	chr1:155879114..155881367-chr1:155902425..155905245,4	MCF-7	breast:
13	chr1:155902799..155907084-chr1:156021354..156025347,11	K562	blood:
14	chr1:155874080..155876407-chr1:155902022..155904119,2	MCF-7	breast:
15	chr1:155902135..155904272-chr1:155989311..155991298,2	MCF-7	breast:
16	chr1:155902926..155905486-chr1:155988342..155992219,3	K562	blood:
17	chr1:155901793..155904687-chr1:155910352..155912592,3	MCF-7	breast:
18	chr1:155902871..155906324-chr1:155958036..155960843,4	K562	blood:
19	chr1:155902972..155905635-chr1:155940527..155942498,2	K562	blood:
20	chr1:155902827..155906202-chr1:155937016..155941458,5	MCF-7	breast:
21	chr1:155826962..155828994-chr1:155903211..155904841,2	K562	blood:
22	chr1:155902875..155906059-chr1:156051194..156053786,3	MCF-7	breast:
23	chr1:155878384..155883302-chr1:155900472..155905868,7	K562	blood:
24	chr1:155902066..155906841-chr1:156030418..156033688,4	MCF-7	breast:
25	chr1:155902617..155905990-chr1:156022859..156025987,6	MCF-7	breast:
26	chr1:155900582..155906000-chr1:156022334..156026632,8	MCF-7	breast:
27	chr1:155902817..155905494-chr1:155972290..155974046,2	MCF-7	breast:
28	chr1:155902826..155904472-chr1:155940527..155942381,2	K562	blood:
29	chr1:155902613..155905963-chr1:155944776..155950602,8	MCF-7	breast:
30	chr1:155902334..155905932-chr1:156022257..156026290,7	K562	blood:
31	chr1:155879409..155881796-chr1:155901375..155905401,4	MCF-7	breast:
32	chr1:155885238..155887590-chr1:155902969..155906233,3	K562	blood:
33	chr1:155902781..155905486-chr1:155988342..155993651,4	K562	blood:
34	chr1:155902096..155906333-chr1:155944635..155950706,8	K562	blood:
35	chr1:155903347..155907384-chr1:155909974..155912355,7	K562	blood:
36	chr1:155902685..155905586-chr1:155957752..155961229,4	MCF-7	breast:
37	chr1:155902760..155905677-chr1:155945999..155951456,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000254726	Chromatin interaction
ENSG00000132698	Chromatin interaction
ENSG00000132718	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000273002	Chromatin interaction
ENSG00000224276	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000252808	Chromatin interaction
ENSG00000116580	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000173080	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11264422	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12024880	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027412	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1749410	0.82[ASN][1000 genomes]
rs2993207	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];0.86[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs488079	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490498	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs539602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639398	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656247	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656737	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670523	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]
rs729022	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7517204	0.82[ASN][1000 genomes]
rs7538214	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs822490	0.83[MEX][hapmap]
rs822504	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs822505	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs822508	0.88[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs822509	0.82[ASN][1000 genomes]
rs860295	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs4661151	RIT1	cis	cerebellum	SCAN
rs4661151	YY1AP1	cis	cerebellum	SCAN
rs4661151	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs4661151	ROBLD3	cis	parietal	SCAN
rs4661151	UBQLN4	trans	parietal	SCAN
rs4661151	FAM189B	cis	cerebellum	SCAN
rs4661151	SPRR3	cis	parietal	SCAN
rs4661151	SLC39A1	cis	cerebellum	SCAN
rs4661151	PRUNE	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155897800-155904000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155899400-155903600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:155900000-155903600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:155900000-155903600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
5	chr1:155900200-155903600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:155900200-155903600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:155900600-155903800	Transcr. at gene 5' and 3'	NHLF	lung
8	chr1:155901000-155904000	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr1:155901000-155904400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:155901200-155903600	Transcr. at gene 5' and 3'	NHEK	skin
11	chr1:155901400-155903600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155901400-155903600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
13	chr1:155901400-155903800	Transcr. at gene 5' and 3'	K562	blood
14	chr1:155902000-155905000	Active TSS	Right Ventricle	heart
15	chr1:155902200-155903600	Flanking Active TSS	HUVEC	blood vessel
16	chr1:155902400-155903600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:155902600-155903600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
18	chr1:155902600-155903600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
19	chr1:155902600-155905000	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:155902800-155903600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
21	chr1:155902800-155903600	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr1:155902800-155903600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:155902800-155903600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:155902800-155903800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:155902800-155904000	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr1:155902800-155904000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:155902800-155904800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:155903000-155903600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:155903000-155903600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:155903000-155903600	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr1:155903000-155903600	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr1:155903000-155903600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
33	chr1:155903000-155903600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr1:155903000-155903600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
35	chr1:155903000-155903600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
36	chr1:155903000-155903800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:155903000-155903800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr1:155903000-155903800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr1:155903000-155903800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:155903000-155903800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr1:155903000-155904000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:155903000-155904200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
43	chr1:155903000-155904600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:155903000-155904600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:155903000-155904600	Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:155903000-155904600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:155903000-155904600	Active TSS	Stomach Mucosa	stomach
48	chr1:155903000-155904600	Active TSS	HSMMtube	muscle
49	chr1:155903000-155904800	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:155903000-155904800	Active TSS	Brain Inferior Temporal Lobe	brain

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