Variant report

Variant	rs859040
Chromosome Location	chr1:95384670-95384671
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10465759	0.85[CEU][hapmap]
rs11801110	0.84[CEU][hapmap]
rs3890785	0.84[CEU][hapmap]
rs6674467	0.85[CEU][hapmap]
rs6678809	0.85[CEU][hapmap]
rs6680551	0.85[CEU][hapmap]
rs6684137	0.85[CEU][hapmap]
rs6697256	0.85[CEU][hapmap]
rs864553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv947291	chr1:95382933-95393244	Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs859040	PTBP2	cis	parietal	SCAN
rs859040	F3	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95329000-95385000	Weak transcription	Colonic Mucosa	Colon
2	chr1:95357800-95390800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:95364000-95388600	Weak transcription	Fetal Brain Male	brain
4	chr1:95364800-95384800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:95368400-95388400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:95368400-95390600	Weak transcription	Fetal Thymus	thymus
7	chr1:95369000-95388200	Weak transcription	Fetal Brain Female	brain
8	chr1:95372800-95385000	Weak transcription	Fetal Kidney	kidney
9	chr1:95375800-95385000	Weak transcription	A549	lung
10	chr1:95376000-95384800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:95376400-95384800	Weak transcription	HUVEC	blood vessel
12	chr1:95376400-95385000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:95376600-95385000	Weak transcription	NHEK	skin
14	chr1:95377200-95385400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:95378200-95385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:95378400-95385200	Weak transcription	Placenta	Placenta
17	chr1:95378600-95384800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:95378600-95385000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:95378600-95388600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:95378800-95384800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:95379200-95384800	Weak transcription	Brain Substantia Nigra	brain
22	chr1:95379200-95384800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:95379400-95384800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:95379800-95385000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:95379800-95385000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:95379800-95385000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:95380000-95384800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:95380200-95384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:95380200-95384800	Weak transcription	Liver	Liver
30	chr1:95380200-95385200	Weak transcription	Gastric	stomach
31	chr1:95381000-95384800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:95381000-95385000	Weak transcription	Brain Anterior Caudate	brain
33	chr1:95381400-95385000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:95381400-95386400	Enhancers	Colon Smooth Muscle	Colon
35	chr1:95381600-95384800	Weak transcription	Pancreas	Pancrea
36	chr1:95381600-95385000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:95381600-95385000	Weak transcription	Spleen	Spleen
38	chr1:95381600-95385200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:95381600-95385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:95381600-95387400	Weak transcription	Psoas Muscle	Psoas
41	chr1:95381800-95384800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:95382000-95384800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:95382000-95385200	Weak transcription	Aorta	Aorta
44	chr1:95382200-95384800	Weak transcription	Small Intestine	intestine
45	chr1:95382200-95385600	Weak transcription	Fetal Stomach	stomach
46	chr1:95382400-95384800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:95382400-95385000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:95382600-95384800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:95382800-95386000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:95383000-95384800	Weak transcription	Lung	lung

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