Variant report

Variant	rs2289190
Chromosome Location	chr1:220273564-220273565
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220266681..220268985-chr1:220272321..220274957,2	K562	blood:
2	chr1:220267849..220270969-chr1:220271218..220274109,4	MCF-7	breast:
3	chr1:220267013..220269382-chr1:220272899..220275972,4	K562	blood:
4	chr1:220267376..220270476-chr1:220271823..220275078,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067704	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11095	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs12037461	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17563262	0.89[CEU][hapmap]
rs17563518	0.89[CEU][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap]
rs17563587	0.89[CEU][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap]
rs2053250	0.83[CEU][hapmap]
rs2164790	0.83[EUR][1000 genomes]
rs3738336	0.89[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs3738337	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59541021	0.83[EUR][1000 genomes]
rs60531981	0.80[EUR][1000 genomes]
rs72747386	0.80[EUR][1000 genomes]
rs9431224	0.86[EUR][1000 genomes]

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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289190	BPNT1	cis	cerebellum	SCAN
rs2289190	RRP15	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268200-220275400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:220268400-220274800	Weak transcription	Psoas Muscle	Psoas
3	chr1:220268400-220277400	Weak transcription	Aorta	Aorta
4	chr1:220268400-220280400	Weak transcription	Fetal Kidney	kidney
5	chr1:220268400-220283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:220268400-220287400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:220268400-220293400	Weak transcription	Stomach Mucosa	stomach
8	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:220268600-220274800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:220268600-220274800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:220268600-220274800	Weak transcription	Right Ventricle	heart
12	chr1:220268600-220274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:220268600-220282600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:220268600-220293800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:220268800-220277400	Weak transcription	Colonic Mucosa	Colon
16	chr1:220269000-220275600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:220269200-220273600	Strong transcription	K562	blood
18	chr1:220269200-220274000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:220269200-220274600	Weak transcription	Left Ventricle	heart
20	chr1:220269200-220274800	Weak transcription	Ovary	ovary
21	chr1:220269200-220275200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:220269200-220275200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:220269200-220275600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:220269200-220276800	Weak transcription	HSMMtube	muscle
25	chr1:220269200-220277400	Weak transcription	Pancreas	Pancrea
26	chr1:220269200-220277600	Weak transcription	Small Intestine	intestine
27	chr1:220269200-220277600	Weak transcription	Thymus	Thymus
28	chr1:220269200-220277800	Weak transcription	Fetal Brain Male	brain
29	chr1:220269200-220279400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:220269200-220279800	Weak transcription	Gastric	stomach
31	chr1:220269200-220280800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:220269200-220282400	Weak transcription	Spleen	Spleen
33	chr1:220269200-220282600	Weak transcription	Esophagus	oesophagus
34	chr1:220269200-220285400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:220269200-220291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:220269200-220291600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:220269200-220292800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:220269200-220293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:220269400-220274000	Strong transcription	Fetal Muscle Leg	muscle
40	chr1:220269400-220275400	Weak transcription	Primary T cells from cord blood	blood
41	chr1:220269400-220277000	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:220269400-220277000	Weak transcription	Hela-S3	cervix
43	chr1:220269400-220277400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:220269400-220278600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:220269400-220278600	Weak transcription	NHLF	lung
46	chr1:220269400-220280400	Weak transcription	Fetal Heart	heart
47	chr1:220269400-220283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:220269400-220284800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:220269400-220284800	Strong transcription	Osteobl	bone
50	chr1:220269400-220291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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