Variant report

Variant	rs867550
Chromosome Location	chr1:155880391-155880392
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155825653..155829252-chr1:155877943..155882760,5	MCF-7	breast:
2	chr1:155879962..155882698-chr1:155885713..155888748,6	MCF-7	breast:
3	chr1:155879661..155882760-chr1:155946571..155949454,3	K562	blood:
4	chr1:155879409..155881796-chr1:155901375..155905401,4	MCF-7	breast:
5	chr1:155878384..155883302-chr1:155900472..155905868,7	K562	blood:
6	chr1:155825368..155829605-chr1:155879516..155883021,7	K562	blood:
7	chr1:155823442..155829143-chr1:155879989..155882670,6	MCF-7	breast:
8	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:
9	chr1:155879114..155881367-chr1:155902425..155905245,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132680	Chromatin interaction
ENSG00000116580	Chromatin interaction
ENSG00000132718	Chromatin interaction
ENSG00000273002	Chromatin interaction
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10796955	0.95[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs10908481	0.82[MEX][hapmap]
rs10908483	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1111102	0.81[CEU][hapmap]
rs11264426	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs11585845	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs12026057	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12037177	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12080846	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12091273	0.89[AFR][1000 genomes]
rs12091361	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12118795	0.86[CEU][hapmap]
rs12144175	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs1889532	0.95[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs1889533	0.82[AMR][1000 genomes]
rs2016251	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2282301	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297649	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs2364403	0.93[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3820594	0.86[MEX][hapmap]
rs4661218	0.95[CEU][hapmap];0.91[MEX][hapmap]
rs66466805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66669006	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6667652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6670477	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670493	0.95[CEU][hapmap]
rs6696019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72708205	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729022	0.83[MEX][hapmap]
rs7528441	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7534858	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs7545308	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs867548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867549	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915178	0.81[CEU][hapmap]
rs915181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs928596	0.95[CEU][hapmap];0.91[MEX][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
rs867550	PRUNE	cis	cerebellum	SCAN
rs867550	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs867550	YY1AP1	cis	cerebellum	SCAN
rs867550	ROBLD3	cis	parietal	SCAN
rs867550	RIT1	cis	Thyroid	GTEx
rs867550	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs867550	HAPLN2	cis	parietal	SCAN
rs867550	RIT1	cis	cerebellum	SCAN
rs867550	SPRR3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155874000-155880400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:155874000-155880400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:155875400-155880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155876800-155880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:155877200-155880400	Weak transcription	Gastric	stomach
6	chr1:155878200-155880400	Weak transcription	Psoas Muscle	Psoas
7	chr1:155879000-155880400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:155879200-155880400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:155879200-155880400	Enhancers	Liver	Liver
10	chr1:155879400-155880800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:155879400-155880800	Transcr. at gene 5' and 3'	Dnd41	blood
12	chr1:155879400-155880800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr1:155879400-155881600	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:155879600-155880400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:155879600-155880400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:155879600-155880800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:155879600-155880800	Flanking Active TSS	NHEK	skin
18	chr1:155879600-155881400	Active TSS	Esophagus	oesophagus
19	chr1:155879800-155880400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:155879800-155880400	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:155879800-155880400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:155879800-155880400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:155879800-155880400	Flanking Active TSS	Fetal Brain Female	brain
24	chr1:155879800-155880400	Enhancers	Pancreas	Pancrea
25	chr1:155879800-155880400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:155879800-155880400	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr1:155879800-155880400	Enhancers	Small Intestine	intestine
28	chr1:155879800-155880400	Enhancers	Spleen	Spleen
29	chr1:155879800-155880400	Flanking Active TSS	A549	lung
30	chr1:155879800-155880600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
31	chr1:155879800-155880600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:155879800-155880600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr1:155879800-155880600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
34	chr1:155879800-155880800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr1:155879800-155880800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr1:155879800-155880800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr1:155879800-155880800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr1:155879800-155880800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:155879800-155881400	Active TSS	Fetal Brain Male	brain
40	chr1:155879800-155881600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:155880000-155880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:155880000-155880400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:155880000-155880400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:155880000-155880400	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr1:155880000-155880400	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr1:155880000-155880400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:155880000-155880400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:155880000-155880400	Enhancers	Stomach Mucosa	stomach
49	chr1:155880000-155880600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:155880000-155880600	Flanking Active TSS	Fetal Lung	lung

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