Variant report

Variant	rs3743201
Chromosome Location	chr15:79274253-79274254
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr15:79274097-79274370	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79266861..79270074-chr15:79272087..79274367,3	K562	blood:
2	chr15:79164464..79167320-chr15:79273608..79277179,4	K562	blood:
3	chr15:79272849..79274455-chr15:79275680..79277693,2	K562	blood:
4	chr15:79272649..79275133-chr15:79307482..79309069,2	MCF-7	breast:
5	chr15:79264746..79267610-chr15:79273645..79276620,3	K562	blood:
6	chr15:79271517..79274349-chr15:79274954..79277693,2	K562	blood:
7	chr15:79268574..79270778-chr15:79272295..79274532,2	K562	blood:
8	chr15:79235640..79237951-chr15:79272936..79275463,2	MCF-7	breast:
9	chr15:79165092..79167959-chr15:79271269..79275481,5	MCF-7	breast:

No data

Variant related genes	Relation type
RASGRF1	TF binding region
ENSG00000058335	Chromatin interaction
ENSG00000185787	Chromatin interaction
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11852922	0.80[EUR][1000 genomes]
rs2230518	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278650	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28566661	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28774671	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743196	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743197	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743198	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784533	0.90[JPT][hapmap]
rs3803544	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55942507	0.80[EUR][1000 genomes]
rs56060107	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6495356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167720	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7167721	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7167730	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7168964	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173329	0.81[CEU][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7174399	0.88[ASW][hapmap];0.94[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7175590	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7175835	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8026309	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8026710	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8033417	0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs8036107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904433	chr15:79243571-79310288	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3743201	C15orf37	cis	cerebellum	SCAN
rs3743201	PSTPIP1	cis	parietal	SCAN
rs3743201	MORF4L1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79244000-79288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:79261200-79280400	Weak transcription	Esophagus	oesophagus
3	chr15:79270000-79278400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:79270400-79274400	Weak transcription	HSMMtube	muscle
5	chr15:79271400-79275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:79271600-79275800	Weak transcription	Lung	lung
7	chr15:79272200-79274800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:79272200-79275200	Weak transcription	HSMM	muscle
9	chr15:79272200-79275600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:79272200-79275600	Weak transcription	Right Ventricle	heart
11	chr15:79272200-79275800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:79272200-79275800	Weak transcription	Placenta	Placenta
13	chr15:79272200-79275800	Weak transcription	Right Atrium	heart
14	chr15:79272200-79276000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:79272200-79276000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:79272200-79276200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:79272200-79280000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:79272200-79280000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:79272200-79280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:79272200-79280200	Weak transcription	Pancreas	Pancrea
21	chr15:79272200-79280400	Weak transcription	Brain Substantia Nigra	brain
22	chr15:79272200-79280600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:79272200-79284400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:79272400-79275000	Weak transcription	HepG2	liver
25	chr15:79272400-79275400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:79272400-79275400	Weak transcription	Spleen	Spleen
27	chr15:79272400-79275800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:79272400-79279600	Weak transcription	Fetal Intestine Large	intestine
29	chr15:79272400-79280200	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:79272400-79286400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:79272600-79280000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:79273000-79274400	ZNF genes & repeats	GM12878-XiMat	blood
33	chr15:79273000-79275200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr15:79273600-79276400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr15:79274000-79276400	Enhancers	Adipose Nuclei	Adipose
36	chr15:79274000-79279400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:79274200-79274400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:79274200-79276400	Enhancers	Monocytes-CD14+_RO01746	blood

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