Variant report

Variant	rs3743197
Chromosome Location	chr15:79270864-79270865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr15:79270733-79272504	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:79268732-79273709	GM12891	blood:	n/a	n/a
3	EBF1	chr15:79270842-79272413	GM12878	blood:	n/a	chr15:79270961-79270970 chr15:79270961-79270971
4	POLR2A	chr15:79270756-79272484	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:79270858-79270882	GM12878	blood:	n/a	n/a
6	ELF1	chr15:79270837-79271873	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:79270861-79272400	GM19193	blood:	n/a	n/a
8	POLR2A	chr15:79268888-79273418	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:79270840-79272689	GM12892	blood:	n/a	n/a
10	EBF1	chr15:79270838-79271754	GM12878	blood:	n/a	chr15:79270961-79270970 chr15:79270961-79270971
11	POLR2A	chr15:79270713-79272515	GM12892	blood:	n/a	n/a
12	POU2F2	chr15:79270835-79271391	GM12878	blood:	n/a	chr15:79271014-79271026
13	RUNX3	chr15:79270841-79271703	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:79270754-79272517	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:79270858-79272371	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79217200..79220348-chr15:79270743..79273551,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177699	TF binding region
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2230518	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278650	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28566661	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28774671	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3743196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743198	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743201	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]
rs3784533	0.90[JPT][hapmap]
rs3803544	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56060107	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6495356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7167720	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7167721	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7167730	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7168964	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173329	0.81[CEU][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs7174399	0.88[ASW][hapmap];0.94[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7175590	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7175835	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8026309	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8026710	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8033417	0.83[EUR][1000 genomes]
rs8036107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3743197	PSTPIP1	cis	parietal	SCAN
rs3743197	MORF4L1	cis	cerebellum	SCAN

Chromatin state (count:33 , 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	chr15:79263600-79271200	Weak transcription	Lung	lung
4	chr15:79263800-79271200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:79264000-79271400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:79264200-79271400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:79264200-79271800	Weak transcription	Brain Angular Gyrus	brain
8	chr15:79265800-79271000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:79268200-79272400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:79268400-79272600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr15:79268800-79273200	Enhancers	Primary B cells from peripheral blood	blood
12	chr15:79269000-79271200	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:79269000-79272400	Enhancers	Primary B cells from cord blood	blood
14	chr15:79269000-79272400	Enhancers	Spleen	Spleen
15	chr15:79269200-79272400	Enhancers	HepG2	liver
16	chr15:79269400-79271600	Weak transcription	Brain Substantia Nigra	brain
17	chr15:79269400-79271600	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:79269800-79272200	Enhancers	Brain Cingulate Gyrus	brain
19	chr15:79270000-79271000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:79270000-79271800	Weak transcription	Brain Anterior Caudate	brain
21	chr15:79270000-79271800	Weak transcription	Fetal Intestine Large	intestine
22	chr15:79270000-79278400	Weak transcription	Fetal Intestine Small	intestine
23	chr15:79270400-79271400	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:79270400-79271400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr15:79270400-79271600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:79270400-79271600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr15:79270400-79271800	Weak transcription	K562	blood
28	chr15:79270400-79272000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:79270400-79274400	Weak transcription	HSMMtube	muscle
30	chr15:79270600-79271000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:79270600-79271800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:79270800-79272800	Flanking Active TSS	GM12878-XiMat	blood
33	chr15:79270800-79274000	Enhancers	Fetal Muscle Trunk	muscle

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