Variant report

Variant	rs4296472
Chromosome Location	chr2:48747079-48747080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48730893..48733076-chr2:48744799..48747082,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10184783	0.85[ASN][1000 genomes]
rs12616834	0.81[ASN][1000 genomes]
rs12620002	0.85[ASN][1000 genomes]
rs13410391	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs2177487	0.81[ASN][1000 genomes]
rs34461314	0.82[ASN][1000 genomes]
rs4293602	0.90[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4528813	0.86[CHB][hapmap]
rs4641991	0.81[ASN][1000 genomes]
rs4952915	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4953572	0.84[CHB][hapmap];0.84[MEX][hapmap]
rs6545046	0.96[EUR][1000 genomes]
rs6733533	0.84[ASN][1000 genomes]
rs7569575	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[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	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4296472	GTF2A1L	cis	Esophagus Muscularis	GTEx
rs4296472	PPP1R21	cis	Thyroid	GTEx
rs4296472	STON1-GTF2A1L	cis	cerebellum	SCAN
rs4296472	UNQ6975	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
2	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
4	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:48728200-48756800	Weak transcription	HMEC	breast
6	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:48732400-48749600	Strong transcription	Primary B cells from cord blood	blood
8	chr2:48736000-48752800	Weak transcription	Small Intestine	intestine
9	chr2:48736200-48749400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr2:48736200-48749400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:48736400-48748400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:48736400-48749600	Strong transcription	Liver	Liver
13	chr2:48736400-48750000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:48736400-48752600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:48736400-48753400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:48736400-48754600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:48736600-48749600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:48736600-48749800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:48736800-48747200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:48736800-48749400	Strong transcription	Fetal Thymus	thymus
21	chr2:48736800-48749600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:48737000-48748200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:48737000-48748600	Strong transcription	Dnd41	blood
24	chr2:48737000-48749600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:48737000-48749600	Strong transcription	Brain Anterior Caudate	brain
26	chr2:48737200-48750600	Strong transcription	Fetal Intestine Large	intestine
27	chr2:48737600-48749800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:48737600-48750200	Strong transcription	Primary T cells from cord blood	blood
29	chr2:48737800-48749400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:48737800-48750000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:48737800-48752000	Strong transcription	Fetal Intestine Small	intestine
32	chr2:48737800-48756200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:48738000-48749600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:48738000-48750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:48738000-48755400	Weak transcription	HUVEC	blood vessel
36	chr2:48738000-48756800	Weak transcription	NH-A	brain
37	chr2:48738200-48753800	Weak transcription	Hela-S3	cervix
38	chr2:48740000-48754400	Weak transcription	NHLF	lung
39	chr2:48740000-48756000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:48740000-48757600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:48740800-48749200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:48740800-48749400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:48741000-48748800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:48741000-48753000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:48742200-48749400	Strong transcription	Thymus	Thymus
46	chr2:48742400-48748200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr2:48742400-48756200	Weak transcription	NHDF-Ad	bronchial
48	chr2:48743000-48749400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:48743000-48754600	Weak transcription	Fetal Kidney	kidney
50	chr2:48743200-48747200	Strong transcription	Fetal Muscle Leg	muscle

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