Variant report

Variant	rs2720447
Chromosome Location	chr4:104026547-104026548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104021157..104023152-chr4:104024263..104027546,3	K562	blood:
2	chr4:104021157..104023420-chr4:104024206..104027148,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10516497	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs11734396	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];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502620	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505012	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12506575	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12508128	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17033423	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17217250	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17283278	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243682	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276974	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276975	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2615538	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2615541	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615542	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][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];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623062	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623063	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2623069	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623076	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623082	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711888	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[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];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711891	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711893	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711894	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2711895	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711896	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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711900	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711901	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720450	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720451	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720452	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720453	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720457	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720463	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720465	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720467	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720470	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816642	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698879	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55708783	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55777543	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58477215	0.87[EUR][1000 genomes]
rs59355472	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs68023422	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830082	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6847142	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847357	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665085	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665089	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72666813	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7435875	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7672974	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9760911	0.82[ASN][1000 genomes]
rs9994654	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2720447	TET2	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104012400-104028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:104019800-104030200	Weak transcription	Esophagus	oesophagus
3	chr4:104021000-104026600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr4:104021000-104027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:104021000-104027200	Weak transcription	K562	blood
6	chr4:104021000-104028000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:104021000-104028200	Weak transcription	Brain Germinal Matrix	brain
8	chr4:104021000-104028600	Weak transcription	HSMM	muscle
9	chr4:104021000-104029800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:104021000-104031600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:104021000-104031600	Weak transcription	Placenta	Placenta
12	chr4:104021000-104033600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:104021000-104049200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:104021000-104049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:104021000-104056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:104021000-104058200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:104021000-104063800	Weak transcription	Fetal Stomach	stomach
18	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
19	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
20	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
21	chr4:104021200-104027000	Weak transcription	Fetal Thymus	thymus
22	chr4:104021200-104027200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:104021200-104027200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:104021200-104027200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:104021200-104027200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:104021200-104027200	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:104021200-104027200	Weak transcription	Thymus	Thymus
28	chr4:104021200-104027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:104021200-104028200	Weak transcription	Primary B cells from cord blood	blood
30	chr4:104021200-104028600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:104021200-104028600	Weak transcription	NHDF-Ad	bronchial
32	chr4:104021200-104028800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:104021200-104028800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:104021200-104029800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:104021200-104030200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:104021200-104030400	Weak transcription	Primary T cells from cord blood	blood
37	chr4:104021200-104032400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:104021200-104032600	Weak transcription	Fetal Kidney	kidney
39	chr4:104021200-104032800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:104021200-104045800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:104021400-104026600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:104021400-104026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:104021400-104027200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:104021400-104027200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:104021400-104027200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:104021400-104027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:104021400-104027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:104021400-104027200	Weak transcription	Dnd41	blood

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