Variant report

Variant	rs3773621
Chromosome Location	chr3:150996434-150996435
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr3:150996390-150996457	GM12878	blood:	n/a	n/a
2	SPI1	chr3:150995973-150996622	HL-60	blood:	n/a	chr3:150996282-150996289 chr3:150996282-150996295 chr3:150996593-150996606 chr3:150996190-150996203

Variant related genes	Relation type
P2RY14	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10513391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935831	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935832	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935833	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935839	0.87[CEU][hapmap]
rs11925037	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11926145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12107539	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12485537	0.85[EUR][1000 genomes]
rs12486265	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12497019	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497330	0.87[CEU][hapmap]
rs12636396	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs12637988	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12639390	0.82[CHB][hapmap]
rs13079391	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095610	0.87[CEU][hapmap]
rs1388617	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16863287	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882013	0.82[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap]
rs2307020	0.87[CEU][hapmap]
rs28527299	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34347156	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34708786	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35144003	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35786948	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732759	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs3806636	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680256	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs4680263	0.96[CHD][hapmap]
rs4680307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680315	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680356	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55705054	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56087525	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62282988	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62283022	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440738	0.87[CEU][hapmap]
rs66524723	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66927386	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6767192	0.87[CEU][hapmap]
rs6784934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6785930	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6790448	0.87[CEU][hapmap]
rs6793898	0.86[CEU][hapmap]
rs6796501	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801155	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6801273	0.87[CEU][hapmap]
rs6804769	0.87[CEU][hapmap]
rs6808091	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7428575	0.87[CEU][hapmap]
rs7618206	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644001	0.87[CEU][hapmap]
rs7648875	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3773621	CLRN1	cis	parietal	SCAN
rs3773621	MED12L	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150977800-151000000	Weak transcription	Placenta	Placenta
2	chr3:150983000-151011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:150983800-151000600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:150984200-150998800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:150984600-151003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:150984600-151003600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:150991400-150998600	Enhancers	Primary T cells from cord blood	blood
9	chr3:150991800-150998800	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:150992000-150997400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:150992200-150997000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:150992600-150996800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:150992600-150997000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:150992800-150996800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:150992800-150997000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:150993000-150996800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr3:150993600-150996800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr3:150993600-150996800	Active TSS	Adipose Nuclei	Adipose
19	chr3:150994400-150997200	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:150994400-150998200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:150994600-150999600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:150994600-151003600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:150995600-150996800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:150995600-150997400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:150995600-150998400	Enhancers	Fetal Thymus	thymus
26	chr3:150995800-150996600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:150995800-150996800	Enhancers	GM12878-XiMat	blood
28	chr3:150995800-150997000	Enhancers	Dnd41	blood
29	chr3:150995800-150997000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:150996000-150996600	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:150996000-150996600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:150996000-150996600	Active TSS	Duodenum Mucosa	Duodenum
33	chr3:150996000-150996600	Enhancers	NHDF-Ad	bronchial
34	chr3:150996000-150996800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:150996200-150996600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr3:150996200-150997200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:150996200-150998600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:150996200-151000200	Weak transcription	Brain Anterior Caudate	brain
39	chr3:150996200-151001000	Weak transcription	Stomach Mucosa	stomach
40	chr3:150996400-150996600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:150996400-150996600	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr3:150996400-150996600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr3:150996400-150996800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:150996400-150997200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:150996400-150997600	Enhancers	Fetal Stomach	stomach
46	chr3:150996400-150997800	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:150996400-150998800	Enhancers	Primary B cells from peripheral blood	blood

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