Variant report

Variant	rs4703797
Chromosome Location	chr5:79365009-79365010
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	chr5:79363092..79365319-chr5:79367879..79369894,2	K562	blood:

Variant related genes	Relation type
ENSG00000113296	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10071934	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10474606	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10514171	0.87[CHB][hapmap]
rs10514174	0.94[CHB][hapmap]
rs11738491	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11739940	0.91[ASN][1000 genomes]
rs12332694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13181102	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16877406	0.87[CHB][hapmap]
rs16877442	1.00[CHB][hapmap]
rs16877468	1.00[CHB][hapmap]
rs17878919	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241826	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813667	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7723567	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9293797	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9293799	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9293800	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4703797	THBS4	cis	cerebellum	SCAN
rs4703797	BHMT	cis	cerebellum	SCAN
rs4703797	THBS4	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79338200-79367600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:79348200-79366400	Weak transcription	Brain Substantia Nigra	brain
3	chr5:79351600-79379200	Weak transcription	Pancreas	Pancrea
4	chr5:79352000-79365200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:79352000-79365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:79352000-79365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:79352400-79378200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:79353200-79365600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:79353600-79365600	Weak transcription	Fetal Intestine Small	intestine
10	chr5:79354600-79378400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:79356400-79366800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:79356600-79373800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr5:79357000-79373200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:79357200-79372800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:79357800-79367800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:79358400-79373600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:79359600-79378200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:79360000-79365200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:79360000-79378200	Weak transcription	Brain Angular Gyrus	brain
20	chr5:79361000-79374400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:79361200-79365600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:79361400-79365200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:79361400-79365400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:79361400-79366600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:79361400-79378400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:79361600-79378400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:79361800-79378400	Strong transcription	Primary T cells from cord blood	blood
28	chr5:79362200-79367200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr5:79362200-79367200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr5:79362600-79377800	Weak transcription	Brain Germinal Matrix	brain
31	chr5:79362600-79378600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:79362800-79367000	Weak transcription	Brain Anterior Caudate	brain
33	chr5:79362800-79372600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:79363000-79378800	Weak transcription	Thymus	Thymus
35	chr5:79363200-79365200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:79363200-79366400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:79363400-79366800	Enhancers	Primary B cells from cord blood	blood
38	chr5:79363600-79366000	Weak transcription	Fetal Intestine Large	intestine
39	chr5:79363800-79365600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:79364000-79365800	Weak transcription	Left Ventricle	heart
41	chr5:79364200-79367200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr5:79364200-79372800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:79364200-79373000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr5:79364400-79366200	Enhancers	Adipose Nuclei	Adipose
45	chr5:79364400-79369200	Enhancers	NHDF-Ad	bronchial
46	chr5:79364400-79378200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:79364600-79366600	Enhancers	Ovary	ovary
48	chr5:79364800-79365600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:79364800-79365600	Weak transcription	Fetal Thymus	thymus
50	chr5:79364800-79366200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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