Variant report

Variant	rs3800119
Chromosome Location	chr6:1885972-1885973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10484694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192948	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs13218267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1570534	0.96[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs1980713	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs2875711	0.87[ASW][hapmap];0.86[MEX][hapmap];0.82[YRI][hapmap]
rs34660383	0.92[EUR][1000 genomes]
rs3778544	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778553	0.82[YRI][hapmap]
rs3800110	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800117	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4959616	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930647	0.87[ASW][hapmap]
rs7776397	0.81[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv883385	chr6:1869592-1915828	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800119	TUBB2A	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:1871000-1895400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:1873800-1893000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:1877600-1915200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:1878600-1890000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:1884400-1886000	Enhancers	Fetal Kidney	kidney
8	chr6:1885000-1886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:1885000-1886000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:1885000-1886200	Enhancers	Aorta	Aorta
11	chr6:1885400-1886600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:1885600-1886000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:1885600-1886200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:1885600-1886200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:1885600-1886200	Enhancers	Fetal Intestine Small	intestine
16	chr6:1885600-1886400	Enhancers	Ovary	ovary
17	chr6:1885600-1886400	Genic enhancers	HepG2	liver
18	chr6:1885600-1886400	Flanking Active TSS	Osteobl	bone
19	chr6:1885600-1886600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:1885600-1886600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:1885600-1886600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:1885800-1886000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:1885800-1886000	Enhancers	Esophagus	oesophagus
24	chr6:1885800-1886200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:1885800-1886200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:1885800-1886200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:1885800-1886200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:1885800-1886200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:1885800-1886200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:1885800-1886200	Enhancers	Brain Substantia Nigra	brain
31	chr6:1885800-1886200	Enhancers	Fetal Intestine Large	intestine
32	chr6:1885800-1886200	Enhancers	Fetal Muscle Trunk	muscle
33	chr6:1885800-1886200	Enhancers	Fetal Muscle Leg	muscle
34	chr6:1885800-1886200	Genic enhancers	Gastric	stomach
35	chr6:1885800-1886200	Enhancers	Pancreas	Pancrea
36	chr6:1885800-1886200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:1885800-1886200	Flanking Active TSS	NH-A	brain
38	chr6:1885800-1886400	Enhancers	HUES6 Cell Line	embryonic stem cell

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