Variant report

Variant	rs2059786
Chromosome Location	chr5:94812698-94812699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94810168..94812031-chr5:94812171..94814242,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10040106	0.87[LWK][hapmap];0.92[YRI][hapmap]
rs1123965	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1162859	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13162779	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545842	0.87[LWK][hapmap];0.92[YRI][hapmap]
rs2560256	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560275	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560276	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560277	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731816	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs2731818	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731828	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731838	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4573018	0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs6556871	0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6556872	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv598954	chr5:94783175-94859599	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2059786	TTC37	cis	cerebellum	SCAN
rs2059786	TTC37	cis	Whole Blood	GTEx
rs2059786	TTC37	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94788800-94822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:94792600-94817800	Weak transcription	Brain Substantia Nigra	brain
3	chr5:94792600-94821800	Weak transcription	Right Ventricle	heart
4	chr5:94794800-94817600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:94795200-94826600	Weak transcription	NHEK	skin
6	chr5:94795400-94814000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:94797000-94817000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:94797000-94819200	Weak transcription	HepG2	liver
9	chr5:94799200-94821600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:94799200-94834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:94802000-94821600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:94802200-94813600	Weak transcription	HMEC	breast
13	chr5:94802200-94816200	Weak transcription	Fetal Brain Male	brain
14	chr5:94804200-94817800	Weak transcription	Fetal Heart	heart
15	chr5:94804600-94816600	Weak transcription	Brain Germinal Matrix	brain
16	chr5:94804600-94817000	Weak transcription	GM12878-XiMat	blood
17	chr5:94804600-94821600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:94804600-94823000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:94804800-94816400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:94804800-94816600	Weak transcription	K562	blood
21	chr5:94807800-94817000	Strong transcription	Primary B cells from cord blood	blood
22	chr5:94808000-94816600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:94808000-94821600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:94808200-94813600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:94808200-94821800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:94808200-94822800	Weak transcription	Psoas Muscle	Psoas
27	chr5:94808600-94812800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:94809000-94823400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:94809800-94823000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr5:94810200-94813200	Strong transcription	HSMM	muscle
31	chr5:94810200-94814400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:94810200-94814400	Strong transcription	Adipose Nuclei	Adipose
33	chr5:94810200-94815400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:94810200-94823000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:94810200-94823000	Strong transcription	Dnd41	blood
36	chr5:94810200-94823000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr5:94810200-94823200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:94810200-94827400	Strong transcription	Fetal Thymus	thymus
39	chr5:94810600-94813000	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:94810600-94813200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr5:94810600-94814200	Strong transcription	HUVEC	blood vessel
42	chr5:94810600-94814400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:94810600-94814600	Strong transcription	Fetal Intestine Large	intestine
44	chr5:94810600-94816800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:94810600-94823000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:94810600-94823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:94810600-94823200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr5:94810600-94827600	Strong transcription	Placenta	Placenta
49	chr5:94810800-94813000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:94810800-94813000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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