Variant report

Variant	rs2639997
Chromosome Location	chr3:141330310-141330311
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	chr3:141084267..141086833-chr3:141329024..141330531,2	K562	blood:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11711375	0.88[JPT][hapmap]
rs11917587	0.88[JPT][hapmap]
rs1493209	0.88[JPT][hapmap]
rs1493210	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851438	0.83[JPT][hapmap]
rs16851441	1.00[JPT][hapmap]
rs16851483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863867	0.88[JPT][hapmap]
rs2035935	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];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2035936	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2640017	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295299	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295300	0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295320	0.88[JPT][hapmap]
rs295321	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34558081	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806646	0.88[JPT][hapmap]
rs3806648	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821710	0.88[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683612	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58025624	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60654199	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61750362	0.90[AFR][1000 genomes]
rs6767158	0.88[JPT][hapmap]
rs6785874	0.88[JPT][hapmap]
rs6795168	0.88[JPT][hapmap]
rs6800122	0.88[JPT][hapmap]
rs6808837	0.88[JPT][hapmap]
rs73871847	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618787	0.90[ASW][hapmap];0.94[LWK][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs7626871	0.88[JPT][hapmap]
rs7627774	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7643837	0.88[JPT][hapmap]
rs9878347	0.83[JPT][hapmap]
rs9879503	0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2639997	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:141313200-141344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:141320400-141331000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:141320400-141333600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:141320400-141337200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:141321600-141331800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:141321800-141342600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:141324000-141333800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:141324200-141333600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:141324200-141336000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:141324600-141332000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:141324800-141332200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:141324800-141334000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:141325000-141332200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:141325000-141338000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:141325600-141333600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:141325600-141335000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:141325800-141333600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:141326000-141332400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:141326000-141333000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:141326200-141332600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:141326400-141332400	Strong transcription	HSMM	muscle
24	chr3:141326600-141334000	Strong transcription	Dnd41	blood
25	chr3:141326600-141334200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:141326600-141335400	Strong transcription	HUVEC	blood vessel
27	chr3:141326800-141330400	Strong transcription	HMEC	breast
28	chr3:141326800-141330400	Strong transcription	NH-A	brain
29	chr3:141326800-141330600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:141326800-141330800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:141326800-141331600	Strong transcription	Fetal Lung	lung
32	chr3:141326800-141331800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:141326800-141332000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:141326800-141332000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr3:141326800-141332200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:141326800-141332400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:141326800-141332400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:141326800-141333200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:141326800-141334000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:141326800-141335600	Strong transcription	Primary B cells from cord blood	blood
41	chr3:141327000-141330400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:141327000-141330400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:141327000-141330400	Strong transcription	Brain Angular Gyrus	brain
44	chr3:141327000-141332000	Strong transcription	NHDF-Ad	bronchial
45	chr3:141327000-141332200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:141327000-141332200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:141327000-141332200	Strong transcription	Adipose Nuclei	Adipose
48	chr3:141327000-141332200	Strong transcription	Liver	Liver
49	chr3:141327000-141332400	Strong transcription	Fetal Thymus	thymus
50	chr3:141327000-141333400	Strong transcription	Placenta	Placenta

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