Variant report

Variant	rs2088170
Chromosome Location	chr12:66782412-66782413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1168300	0.86[CEU][hapmap]
rs1168308	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs1168309	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs1168310	0.92[CEU][hapmap]
rs1168311	0.92[CEU][hapmap];0.88[MEX][hapmap]
rs1168327	0.92[CEU][hapmap]
rs1168328	0.92[CEU][hapmap]
rs1168329	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs1177555	0.92[CEU][hapmap]
rs1183272	0.92[CEU][hapmap]
rs1185244	0.92[CEU][hapmap]
rs2172881	0.81[EUR][1000 genomes]
rs6581677	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs6581678	0.81[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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2088170	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs2088170	IRAK3	cis	parietal	SCAN
rs2088170	HELB	cis	cerebellum	SCAN
rs2088170	HELB	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66710200-66792800	Weak transcription	Fetal Kidney	kidney
2	chr12:66738000-66792800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:66743000-66787600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:66760200-66783200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:66763600-66785200	Weak transcription	Brain Germinal Matrix	brain
6	chr12:66764200-66787200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:66765800-66786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:66766200-66785800	Weak transcription	Fetal Brain Female	brain
9	chr12:66771000-66785000	Weak transcription	Placenta	Placenta
10	chr12:66775200-66793000	Weak transcription	Esophagus	oesophagus
11	chr12:66780800-66792800	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:66781200-66782600	Weak transcription	Aorta	Aorta
13	chr12:66781200-66783800	Weak transcription	Pancreas	Pancrea
14	chr12:66781200-66785400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:66781200-66785400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:66781200-66786000	Weak transcription	Fetal Brain Male	brain
17	chr12:66781400-66785000	Weak transcription	Primary T cells from cord blood	blood
18	chr12:66781400-66785600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:66781400-66792000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:66781600-66785000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:66781600-66792800	Weak transcription	Adipose Nuclei	Adipose
22	chr12:66781800-66785200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:66782000-66783000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:66782000-66783400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:66782000-66787800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:66782200-66783000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr12:66782200-66792800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:66782400-66782800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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