Variant report

Variant	rs2893930
Chromosome Location	chr6:27738806-27738807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27734440..27736801-chr6:27737530..27740059,2	MCF-7	breast:
2	chr6:27738620..27740539-chr6:27758419..27760190,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10214440	0.81[EUR][1000 genomes]
rs10484401	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13211701	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs169262	0.88[ASN][1000 genomes]
rs1985099	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200468	0.89[ASN][1000 genomes]
rs200474	0.84[ASN][1000 genomes]
rs200475	0.84[ASN][1000 genomes]
rs200476	0.87[ASN][1000 genomes]
rs2092075	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2179094	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179095	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2394000	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2394002	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893929	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893931	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34752872	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35069907	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35957409	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4140646	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711163	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713121	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901520	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902689	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6914924	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6922574	0.81[EUR][1000 genomes]
rs6930992	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs742046	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs742047	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs760587	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756968	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7759217	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7760523	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7772027	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7773070	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776351	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283880	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9283881	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9283882	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9283883	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295740	0.83[ASN][1000 genomes]
rs9295742	0.82[EUR][1000 genomes]
rs9295743	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9295746	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348774	0.83[ASN][1000 genomes]
rs9348775	0.82[EUR][1000 genomes]
rs9357045	0.83[ASN][1000 genomes]
rs9366700	0.82[EUR][1000 genomes]
rs9366702	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368528	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368529	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368530	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380010	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380011	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380012	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393847	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393848	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9461401	0.81[EUR][1000 genomes]
rs9461405	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9461406	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468200	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468201	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468203	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468204	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468206	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468214	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468217	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468219	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9468220	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468223	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468229	0.83[EUR][1000 genomes];0.91[ASN][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2893930	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2893930	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2893930	AL022393.7	cis	Muscle Skeletal	GTEx
rs2893930	OR2B8P	cis	Thyroid	GTEx
rs2893930	BTN2A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27730600-27740000	Weak transcription	Spleen	Spleen
3	chr6:27730800-27739000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:27730800-27740000	Weak transcription	Primary T cells from cord blood	blood
5	chr6:27737400-27739000	Weak transcription	K562	blood
6	chr6:27737400-27739600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:27738200-27740200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
8	chr6:27738400-27739200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr6:27738600-27739000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:27738600-27739400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:27738600-27739800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:27738600-27739800	Enhancers	Fetal Intestine Large	intestine
13	chr6:27738600-27741600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:27738800-27739000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr6:27738800-27739000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
17	chr6:27738800-27739200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
18	chr6:27738800-27739400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr6:27738800-27739400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
20	chr6:27738800-27739400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr6:27738800-27740000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr6:27738800-27740800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr6:27738800-27741800	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links