Variant report

Variant	rs2622770
Chromosome Location	chr15:51971322-51971323
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	POLR2A	chr15:51971255-51971339	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:51970627..51972181-chr15:52008855..52011853,2	MCF-7	breast:
2	chr15:51970684..51971589-chr15:52068849..52069771,2	MCF-7	breast:
3	chr15:51968757..51971365-chr15:51975638..51977391,2	MCF-7	breast:

Variant related genes	Relation type
SCG3	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1010486	0.82[ASN][1000 genomes]
rs1017679	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10519314	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10519315	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10519316	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10519318	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10519319	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10519320	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10519321	0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10851501	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11070861	0.90[EUR][1000 genomes]
rs12324531	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs12441057	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12708427	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12901452	1.00[CEU][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12904173	0.90[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs12904583	0.83[EUR][1000 genomes]
rs1378892	0.99[EUR][1000 genomes]
rs1378893	0.98[EUR][1000 genomes]
rs1378894	0.93[EUR][1000 genomes]
rs1378895	0.93[EUR][1000 genomes]
rs1456295	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456297	0.98[EUR][1000 genomes]
rs1471072	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1531157	0.88[EUR][1000 genomes]
rs1551657	0.81[EUR][1000 genomes]
rs16964465	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs16964476	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs17524750	0.83[EUR][1000 genomes]
rs17524906	0.95[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs17648565	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs17648801	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs17705035	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1840707	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902595	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1902596	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2124588	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2124589	0.94[ASN][1000 genomes]
rs2124590	0.94[ASN][1000 genomes]
rs2252220	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2305709	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2305711	0.94[ASN][1000 genomes]
rs2305712	0.81[ASN][1000 genomes]
rs2305715	0.94[ASN][1000 genomes]
rs2305719	0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2414112	0.91[EUR][1000 genomes]
rs2606134	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606136	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2606137	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606138	0.95[CEU][hapmap];1.00[EUR][1000 genomes]
rs2606139	1.00[EUR][1000 genomes]
rs2606141	0.95[EUR][1000 genomes]
rs2606143	0.95[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs2606145	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606146	1.00[CEU][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2607110	0.86[EUR][1000 genomes]
rs2607112	0.91[EUR][1000 genomes]
rs2607116	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2607117	0.84[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2622768	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2622769	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28408214	0.87[EUR][1000 genomes]
rs28555597	0.81[MEX][hapmap]
rs3214014	0.94[ASN][1000 genomes]
rs34448759	0.83[EUR][1000 genomes]
rs34532503	0.82[EUR][1000 genomes]
rs34662965	0.81[EUR][1000 genomes]
rs34929849	0.82[EUR][1000 genomes]
rs35011964	0.84[EUR][1000 genomes]
rs3764220	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3765067	0.92[ASN][1000 genomes]
rs3809498	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3816544	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs41286490	0.94[ASN][1000 genomes]
rs41286492	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4465557	0.86[EUR][1000 genomes]
rs4774594	0.85[EUR][1000 genomes]
rs4775954	0.95[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs55725532	0.83[EUR][1000 genomes]
rs60337239	0.94[ASN][1000 genomes]
rs60437890	0.94[ASN][1000 genomes]
rs60934476	0.94[ASN][1000 genomes]
rs6493507	0.87[EUR][1000 genomes]
rs6493511	0.95[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs6493512	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6493514	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[EUR][1000 genomes]
rs7163359	0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs716986	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174397	0.81[ASN][1000 genomes]
rs7180329	0.81[EUR][1000 genomes]
rs7181921	0.86[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8023804	0.94[ASN][1000 genomes]
rs8025974	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8027162	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8029731	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs897581	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs956171	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9672605	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9944266	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2622770	TMOD2	cis	parietal	SCAN
rs2622770	BCL2L10	cis	parietal	SCAN
rs2622770	DMXL2	cis	lymphoblastoid	seeQTL
rs2622770	SCG3	cis	parietal	SCAN
rs2622770	SCG3	cis	cerebellum	SCAN
rs2622770	ATP8B4	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51965600-51972200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:51966600-51973400	Weak transcription	Right Atrium	heart
3	chr15:51967400-51973000	Weak transcription	K562	blood
4	chr15:51967800-51973000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:51968800-51973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:51970000-51971800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:51970000-51972000	Weak transcription	Brain Angular Gyrus	brain
8	chr15:51970000-51972000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:51970200-51972200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:51971200-51972000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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