Variant report

Variant	rs34402524
Chromosome Location	chr4:106196829-106196830
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11728350	0.95[GIH][hapmap];0.83[EUR][1000 genomes]
rs1391438	0.84[MKK][hapmap]
rs1391441	0.84[MKK][hapmap]
rs1498125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1498126	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17035310	0.90[GIH][hapmap];0.84[EUR][1000 genomes]
rs17320054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17430251	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508261	0.87[ASW][hapmap];0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4464576	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56185013	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6825684	0.95[GIH][hapmap];0.85[EUR][1000 genomes]
rs72665951	0.82[ASN][1000 genomes]
rs763480	0.85[GIH][hapmap];0.83[EUR][1000 genomes]

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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34402524	TET2	cis	cerebellum	SCAN
rs34402524	BDH2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106154000-106198800	Weak transcription	Hela-S3	cervix
2	chr4:106178000-106201000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:106179200-106201000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:106180200-106199000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:106180400-106198800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106187200-106202000	Weak transcription	Stomach Mucosa	stomach
7	chr4:106188800-106199800	Strong transcription	GM12878-XiMat	blood
8	chr4:106189200-106197800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr4:106189400-106198400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:106189400-106198600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:106189600-106198000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:106189600-106198200	Strong transcription	Placenta	Placenta
13	chr4:106189600-106198400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:106189800-106197600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:106190000-106197800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:106190000-106198600	Strong transcription	Fetal Thymus	thymus
17	chr4:106190200-106197800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:106190200-106197800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:106190200-106197800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:106190200-106197800	Strong transcription	Fetal Lung	lung
21	chr4:106190200-106198000	Strong transcription	Liver	Liver
22	chr4:106190200-106198800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:106190400-106197800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:106190400-106198000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:106190400-106198000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:106190400-106198000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:106190400-106198000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr4:106190400-106198400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:106190400-106198800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:106190400-106199000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:106190400-106199000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:106190600-106197600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:106190600-106197800	Strong transcription	Adipose Nuclei	Adipose
34	chr4:106190600-106197800	Strong transcription	Brain Anterior Caudate	brain
35	chr4:106190600-106198000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:106190600-106198000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:106190600-106198200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr4:106190800-106197400	Strong transcription	Colon Smooth Muscle	Colon
39	chr4:106190800-106198000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:106190800-106198600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr4:106190800-106199200	Strong transcription	HSMM	muscle
42	chr4:106191000-106197000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:106191000-106199000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:106191400-106197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:106191600-106198000	Weak transcription	K562	blood
46	chr4:106191600-106198200	Strong transcription	Primary B cells from cord blood	blood
47	chr4:106192000-106199000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:106193200-106198000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:106193400-106197800	Strong transcription	NHDF-Ad	bronchial
50	chr4:106194400-106198600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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