Variant report

Variant	rs1036869
Chromosome Location	chr13:76370195-76370196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1570556	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2031241	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2031242	0.81[ASN][1000 genomes]
rs2120067	0.83[EUR][1000 genomes]
rs2120068	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274062	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4885348	0.84[EUR][1000 genomes]
rs4885349	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139507	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7320900	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7321748	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7322414	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7326714	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7331429	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7992526	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9530467	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9530473	0.82[GIH][hapmap]
rs9544043	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9573658	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9573659	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1036869	TBC1D4	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76338800-76371000	Weak transcription	Fetal Thymus	thymus
2	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr13:76350000-76371000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr13:76353400-76370600	Weak transcription	Primary T cells from cord blood	blood
5	chr13:76355600-76370800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr13:76358200-76370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr13:76358200-76371400	Weak transcription	NHEK	skin
8	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:76361800-76377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:76362000-76376600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:76362600-76377000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:76363000-76377000	Weak transcription	GM12878-XiMat	blood
13	chr13:76363200-76370800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:76363200-76371000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:76363200-76372400	Weak transcription	HMEC	breast
16	chr13:76363200-76376400	Weak transcription	Esophagus	oesophagus
17	chr13:76363200-76381800	Weak transcription	Fetal Stomach	stomach
18	chr13:76363400-76371600	Weak transcription	Colonic Mucosa	Colon
19	chr13:76363600-76371400	Weak transcription	Small Intestine	intestine
20	chr13:76364200-76370200	Weak transcription	NH-A	brain
21	chr13:76364600-76385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:76364800-76371600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:76365400-76370800	Weak transcription	Fetal Muscle Leg	muscle
24	chr13:76366400-76372800	Weak transcription	Right Ventricle	heart
25	chr13:76366400-76376600	Weak transcription	Left Ventricle	heart
26	chr13:76366400-76380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:76366800-76370600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:76366800-76374800	Weak transcription	Aorta	Aorta
29	chr13:76366800-76376600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:76366800-76379400	Weak transcription	Pancreas	Pancrea
31	chr13:76366800-76379400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr13:76366800-76380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:76366800-76380200	Weak transcription	Lung	lung
34	chr13:76367000-76370800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr13:76367000-76371000	Weak transcription	Psoas Muscle	Psoas
36	chr13:76367000-76372000	Weak transcription	Gastric	stomach
37	chr13:76367000-76374000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr13:76367000-76377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr13:76367000-76379800	Weak transcription	Brain Angular Gyrus	brain
40	chr13:76367000-76380200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr13:76367000-76387000	Weak transcription	Ovary	ovary
42	chr13:76367200-76370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:76367200-76370800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr13:76367200-76370800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:76367200-76370800	Weak transcription	Thymus	Thymus
46	chr13:76367200-76370800	Weak transcription	NHDF-Ad	bronchial
47	chr13:76367200-76371000	Weak transcription	Brain Anterior Caudate	brain
48	chr13:76367200-76371200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr13:76367200-76371400	Weak transcription	Stomach Mucosa	stomach
50	chr13:76367200-76371400	Weak transcription	NHLF	lung

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