Variant report

Variant	rs7173329
Chromosome Location	chr15:79270451-79270452
allele	C/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	STAT5A	chr15:79268845-79270495	GM12878	blood:	n/a	n/a
2	BCLAF1	chr15:79269028-79270502	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:79268732-79273709	GM12891	blood:	n/a	n/a
4	MTA3	chr15:79268702-79270639	GM12878	blood:	n/a	n/a
5	RELA	chr15:79268995-79270535	GM12891	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
6	RUNX3	chr15:79268981-79270521	GM12878	blood:	n/a	n/a
7	POU2F2	chr15:79269320-79270524	GM12878	blood:	n/a	chr15:79270113-79270121 chr15:79270110-79270125
8	POU2F2	chr15:79269943-79270494	GM12891	blood:	n/a	chr15:79270113-79270121 chr15:79270110-79270125
9	RELA	chr15:79269012-79270509	GM19099	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
10	FOXM1	chr15:79269285-79270478	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:79270287-79270527	GM12878	blood:	n/a	n/a
12	MTA3	chr15:79269225-79270481	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:79268888-79273418	GM12878	blood:	n/a	n/a
14	IKZF1	chr15:79269075-79270503	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr15:79268944-79270500	GM12878	blood:	n/a	n/a
16	ATF2	chr15:79269323-79270494	GM12878	blood:	n/a	n/a
17	POLR2A	chr15:79268880-79270498	GM19193	blood:	n/a	n/a
18	POLR2A	chr15:79268749-79270549	GM12892	blood:	n/a	n/a
19	POLR2A	chr15:79268822-79270585	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:79268960-79270470	GM12892	blood:	n/a	n/a
21	POLR2A	chr15:79269975-79270527	GM12892	blood:	n/a	n/a
22	MAX	chr15:79269219-79270461	GM12878	blood:	n/a	n/a
23	PML	chr15:79268954-79270494	GM12878	blood:	n/a	n/a
24	RUNX3	chr15:79268944-79270524	GM12878	blood:	n/a	n/a
25	EBF1	chr15:79270025-79270535	GM12878	blood:	n/a	n/a
26	RELA	chr15:79268952-79270509	GM18505	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
27	NFIC	chr15:79269001-79270511	GM12878	blood:	n/a	n/a
28	RELA	chr15:79268948-79270472	GM18951	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
29	ZNF384	chr15:79270209-79270616	GM12878	blood:	n/a	n/a
30	RELA	chr15:79268795-79270520	GM10847	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
31	NFIC	chr15:79268968-79270501	GM12878	blood:	n/a	n/a
32	RELA	chr15:79269113-79270533	GM15510	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
33	POLR2A	chr15:79268799-79270561	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79268574..79270778-chr15:79272295..79274532,2	K562	blood:

Variant related genes	Relation type
ENSG00000177699	TF binding region

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

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

rs_ID	r²[population]
rs1036378	0.97[ASN][1000 genomes]
rs1867315	0.83[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2230518	0.89[EUR][1000 genomes]
rs2278650	0.95[CEU][hapmap]
rs28566661	0.89[EUR][1000 genomes]
rs28774671	0.81[EUR][1000 genomes]
rs3743196	0.86[EUR][1000 genomes]
rs3743197	0.81[CEU][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs3743198	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs3743200	0.81[CEU][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs3743201	0.81[CEU][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs3803544	0.90[EUR][1000 genomes]
rs3825928	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4778753	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs56060107	0.81[EUR][1000 genomes]
rs6495356	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7168964	0.95[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7174399	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7175590	0.81[EUR][1000 genomes]
rs7175835	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs8026309	0.83[EUR][1000 genomes]
rs8026710	0.82[EUR][1000 genomes]
rs8033417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036107	0.85[EUR][1000 genomes]
rs894783	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][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
rs7173329	PSTPIP1	cis	parietal	SCAN
rs7173329	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	chr15:79268800-79270600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:79268800-79273200	Enhancers	Primary B cells from peripheral blood	blood
13	chr15:79269000-79270600	Flanking Active TSS	GM12878-XiMat	blood
14	chr15:79269000-79271200	Enhancers	Duodenum Mucosa	Duodenum
15	chr15:79269000-79272400	Enhancers	Primary B cells from cord blood	blood
16	chr15:79269000-79272400	Enhancers	Spleen	Spleen
17	chr15:79269200-79272400	Enhancers	HepG2	liver
18	chr15:79269400-79271600	Weak transcription	Brain Substantia Nigra	brain
19	chr15:79269400-79271600	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:79269800-79270800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:79269800-79272200	Enhancers	Brain Cingulate Gyrus	brain
22	chr15:79270000-79271000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:79270000-79271800	Weak transcription	Brain Anterior Caudate	brain
24	chr15:79270000-79271800	Weak transcription	Fetal Intestine Large	intestine
25	chr15:79270000-79278400	Weak transcription	Fetal Intestine Small	intestine
26	chr15:79270400-79270600	Enhancers	Primary hematopoietic stem cells	blood
27	chr15:79270400-79271400	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:79270400-79271400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:79270400-79271600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:79270400-79271600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr15:79270400-79271800	Weak transcription	K562	blood
32	chr15:79270400-79272000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:79270400-79274400	Weak transcription	HSMMtube	muscle

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