Variant report

Variant	rs2031562
Chromosome Location	chr10:27150873-27150874
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	BHLHE40	chr10:27149621-27150934	K562	blood:	n/a	chr10:27149646-27149662

No.	Distal block	Cell Line	Cell type
1	chr10:26986021..26987940-chr10:27149008..27151636,2	MCF-7	breast:
2	chr10:26985918..26987566-chr10:27148462..27151237,2	K562	blood:
3	chr10:27149519..27151430-chr10:27442633..27444807,2	K562	blood:

Variant related genes	Relation type
ABI1	TF binding region
ENSG00000136758	Chromatin interaction
ENSG00000120539	Chromatin interaction
ENSG00000148459	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1031858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741117	0.87[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741119	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741121	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10764638	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs10764639	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10764641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10764643	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10829063	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10829064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10829071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12221102	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1324637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1409130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1542553	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1543849	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1590445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1998631	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1998632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1998634	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2148110	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2182293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2368184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2368185	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2505969	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3802609	0.82[MKK][hapmap]
rs3802612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3916988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4376804	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4747575	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4749185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6482575	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7078119	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7078227	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7895417	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7895559	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7907630	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7915128	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2031562	WAC	cis	parietal	SCAN
rs2031562	LYZL2	cis	cerebellum	SCAN
rs2031562	MYO3A	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27147400-27151000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:27150000-27151000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr10:27150000-27151000	Enhancers	Fetal Thymus	thymus
4	chr10:27150000-27153600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr10:27150000-27155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:27150200-27151000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:27150200-27151000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:27150600-27151000	Enhancers	Pancreas	Pancrea
9	chr10:27150600-27151000	Enhancers	Dnd41	blood
10	chr10:27150600-27152600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:27150600-27153000	Weak transcription	Right Atrium	heart
12	chr10:27150800-27151000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr10:27150800-27151000	Enhancers	HepG2	liver
14	chr10:27150800-27151000	Active TSS	K562	blood
15	chr10:27150800-27151800	Weak transcription	Fetal Brain Female	brain
16	chr10:27150800-27152200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr10:27150800-27155600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:27150800-27155800	Weak transcription	NHEK	skin
19	chr10:27150800-27157200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:27150800-27157800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:27150800-27157800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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