Variant report

Variant	rs3110060
Chromosome Location	chr17:28652914-28652915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:28652524..28654952-chr17:28666321..28667913,2	K562	blood:
2	chr17:28438776..28441159-chr17:28651258..28653956,2	K562	blood:
3	chr17:28641163..28643562-chr17:28651440..28652992,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11656408	0.85[ASN][1000 genomes]
rs12938714	0.87[ASN][1000 genomes]
rs12939390	0.87[ASN][1000 genomes]
rs12941223	0.87[ASN][1000 genomes]
rs2321706	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3103303	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103306	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110452	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3110454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34353378	0.85[ASN][1000 genomes]
rs34622227	0.87[ASN][1000 genomes]
rs35724800	0.81[ASN][1000 genomes]
rs36000555	0.87[ASN][1000 genomes]
rs36048853	0.91[ASN][1000 genomes]
rs3764449	0.87[ASN][1000 genomes]
rs7208052	0.81[ASN][1000 genomes]
rs7342921	0.85[ASN][1000 genomes]
rs8080149	0.85[ASN][1000 genomes]
rs998087	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543300	chr17:28620420-28659310	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3110060	BLMH	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28639800-28653800	Weak transcription	Fetal Intestine Large	intestine
2	chr17:28644000-28667000	Weak transcription	Colonic Mucosa	Colon
3	chr17:28644200-28672600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:28644400-28658400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr17:28645600-28653800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr17:28648000-28663800	Weak transcription	Spleen	Spleen
7	chr17:28649200-28653800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:28649800-28653800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:28651000-28657800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:28651200-28653000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr17:28651800-28653000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:28651800-28653000	Enhancers	Fetal Intestine Small	intestine
13	chr17:28651800-28655600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr17:28651800-28657000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:28652200-28655600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:28652200-28656400	Weak transcription	Primary T cells from cord blood	blood
17	chr17:28652600-28653000	Enhancers	Adipose Nuclei	Adipose
18	chr17:28652600-28656400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:28652800-28653000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr17:28652800-28653800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr17:28652800-28655600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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