Variant report

Variant	rs6906890
Chromosome Location	chr6:12961220-12961221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10948372	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11755825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756003	0.91[EUR][1000 genomes]
rs11759412	0.82[AMR][1000 genomes]
rs13194360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34175679	0.91[EUR][1000 genomes]
rs35266083	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713382	0.84[AMR][1000 genomes]
rs36049381	0.89[EUR][1000 genomes]
rs4129937	0.88[GIH][hapmap]
rs4236093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4331981	0.97[GIH][hapmap]
rs4588689	0.90[EUR][1000 genomes]
rs4711897	0.84[AMR][1000 genomes]
rs4715045	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs59778206	0.82[ASN][1000 genomes]
rs62386820	0.90[EUR][1000 genomes]
rs62386821	0.89[EUR][1000 genomes]
rs6458568	0.81[JPT][hapmap]
rs6458577	0.86[ASN][1000 genomes]
rs66820937	0.91[EUR][1000 genomes]
rs6906017	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6923878	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs6929107	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7757180	0.86[ASN][1000 genomes]
rs7769758	0.86[ASN][1000 genomes]
rs7775566	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs7775710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9395336	0.85[GIH][hapmap]
rs9473070	0.84[ASN][1000 genomes]
rs9473082	0.86[ASN][1000 genomes]
rs9473086	0.81[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs9473120	0.81[JPT][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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6906890	HIVEP1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12957200-12961400	Active TSS	Aorta	Aorta
2	chr6:12958200-12962200	Weak transcription	Spleen	Spleen
3	chr6:12958200-12963000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:12958400-12962800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:12958600-12963200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:12958800-12962400	Weak transcription	Pancreas	Pancrea
7	chr6:12958800-12962800	Weak transcription	NHEK	skin
8	chr6:12958800-12963200	Weak transcription	NHLF	lung
9	chr6:12959000-12962000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:12959000-12962800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:12959000-12962800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:12959000-12963000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:12959000-12963000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:12959000-12963000	Weak transcription	Fetal Stomach	stomach
15	chr6:12959000-12963000	Weak transcription	HSMMtube	muscle
16	chr6:12959000-12963000	Weak transcription	NH-A	brain
17	chr6:12959000-12963000	Weak transcription	NHDF-Ad	bronchial
18	chr6:12959200-12961600	Enhancers	Brain Anterior Caudate	brain
19	chr6:12959200-12962000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:12959200-12962000	Weak transcription	Right Ventricle	heart
21	chr6:12959200-12962200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:12959200-12962200	Weak transcription	Right Atrium	heart
23	chr6:12959200-12962400	Weak transcription	HSMM	muscle
24	chr6:12959200-12963000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:12959200-12963400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:12959200-12964000	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:12959200-12968000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:12959400-12962000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:12959400-12962000	Weak transcription	Lung	lung
30	chr6:12960000-12962200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:12960200-12962400	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:12960200-12962400	Enhancers	Fetal Heart	heart
33	chr6:12960200-12962800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:12960400-12962400	Enhancers	Stomach Smooth Muscle	stomach
35	chr6:12960600-12961400	Enhancers	Left Ventricle	heart
36	chr6:12960600-12963800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:12960800-12962600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:12960800-12962600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:12960800-12962600	Enhancers	HUVEC	blood vessel
40	chr6:12961000-12961800	Weak transcription	Brain Angular Gyrus	brain
41	chr6:12961000-12962200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr6:12961000-12963400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:12961000-12968400	Weak transcription	Brain Substantia Nigra	brain

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