Variant report

Variant	rs6669249
Chromosome Location	chr1:95531373-95531374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10747462	0.90[JPT][hapmap]
rs10874901	0.82[ASW][hapmap];0.90[JPT][hapmap]
rs11165285	0.82[ASW][hapmap];0.90[JPT][hapmap]
rs11165290	0.90[JPT][hapmap]
rs11810584	0.94[JPT][hapmap]
rs12082888	0.90[JPT][hapmap]
rs12717801	0.94[JPT][hapmap]
rs12724815	0.95[JPT][hapmap]
rs3890845	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4335417	0.81[ASN][1000 genomes]
rs4427415	0.95[JPT][hapmap]
rs4950059	0.95[JPT][hapmap]

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	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6669249	PTBP2	cis	parietal	SCAN
rs6669249	GFI1	cis	parietal	SCAN
rs6669249	C1orf146	cis	cerebellum	SCAN
rs6669249	FNBP1L	cis	parietal	SCAN
rs6669249	FNBP1L	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95488200-95537600	Weak transcription	Right Ventricle	heart
2	chr1:95505600-95537400	Weak transcription	Right Atrium	heart
3	chr1:95506000-95537800	Weak transcription	Pancreas	Pancrea
4	chr1:95509400-95532800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:95509400-95534200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:95515600-95535800	Weak transcription	Fetal Lung	lung
7	chr1:95516000-95537200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:95516200-95532600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:95517400-95537800	Weak transcription	Esophagus	oesophagus
10	chr1:95518000-95537000	Weak transcription	Psoas Muscle	Psoas
11	chr1:95518000-95537200	Weak transcription	HSMM	muscle
12	chr1:95521600-95537400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:95523200-95537600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:95523400-95532600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:95523400-95537800	Weak transcription	Left Ventricle	heart
16	chr1:95523600-95534400	Weak transcription	Small Intestine	intestine
17	chr1:95523600-95537200	Weak transcription	NHLF	lung
18	chr1:95523800-95537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:95523800-95537200	Weak transcription	HSMMtube	muscle
20	chr1:95523800-95537800	Weak transcription	Fetal Thymus	thymus
21	chr1:95524000-95537200	Weak transcription	NH-A	brain
22	chr1:95524400-95534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:95524400-95537200	Weak transcription	Osteobl	bone
24	chr1:95524600-95532800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:95524600-95537400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:95524600-95537600	Weak transcription	Colonic Mucosa	Colon
27	chr1:95524600-95537600	Weak transcription	Placenta	Placenta
28	chr1:95525000-95537200	Weak transcription	Primary B cells from cord blood	blood
29	chr1:95525000-95537400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:95525200-95537400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:95525800-95537600	Weak transcription	Fetal Brain Male	brain
32	chr1:95526000-95537400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:95526600-95532600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:95526600-95532600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:95526600-95537400	Weak transcription	HMEC	breast
36	chr1:95526800-95537200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:95527200-95531600	Weak transcription	HepG2	liver
38	chr1:95527200-95537200	Weak transcription	Fetal Kidney	kidney
39	chr1:95527400-95531800	Weak transcription	GM12878-XiMat	blood
40	chr1:95527400-95534400	Weak transcription	Stomach Mucosa	stomach
41	chr1:95527800-95531600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:95528000-95531600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:95528200-95532200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:95528200-95537200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:95528200-95537200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:95528200-95537200	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:95528200-95537400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:95528400-95532600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:95528600-95537400	Weak transcription	Fetal Brain Female	brain
50	chr1:95528800-95532600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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