Variant report

Variant	rs35501037
Chromosome Location	chr6:27739566-27739567
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27734440..27736801-chr6:27737530..27740059,2	MCF-7	breast:
2	chr6:27739073..27741027-chr6:27745777..27747654,2	MCF-7	breast:
3	chr6:27739033..27741746-chr6:27859741..27864779,4	MCF-7	breast:
4	chr6:27738868..27742221-chr6:27743370..27745719,4	MCF-7	breast:
5	chr6:27738620..27740539-chr6:27758419..27760190,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10484399	0.81[EUR][1000 genomes]
rs13192965	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13193480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13194781	0.89[EUR][1000 genomes]
rs13195728	0.92[EUR][1000 genomes]
rs13199649	0.87[EUR][1000 genomes]
rs13199772	0.89[EUR][1000 genomes]
rs13199906	0.89[EUR][1000 genomes]
rs13202291	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13202295	1.00[EUR][1000 genomes]
rs13202775	0.87[EUR][1000 genomes]
rs13210634	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13212318	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13212651	0.89[EUR][1000 genomes]
rs13215275	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13216117	0.85[EUR][1000 genomes]
rs13217620	0.94[EUR][1000 genomes]
rs13218875	0.81[EUR][1000 genomes]
rs17693963	0.82[EUR][1000 genomes]
rs17695758	0.89[EUR][1000 genomes]
rs17749927	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17750747	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751184	0.92[EUR][1000 genomes]
rs17763089	0.89[EUR][1000 genomes]
rs200481	0.83[EUR][1000 genomes]
rs200482	0.81[EUR][1000 genomes]
rs200483	0.83[EUR][1000 genomes]
rs200485	0.83[EUR][1000 genomes]
rs200489	0.83[EUR][1000 genomes]
rs200490	0.81[EUR][1000 genomes]
rs200497	0.81[EUR][1000 genomes]
rs200501	0.83[EUR][1000 genomes]
rs2747054	0.83[EUR][1000 genomes]
rs28360499	0.84[EUR][1000 genomes]
rs34064842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34105070	0.87[EUR][1000 genomes]
rs34194357	0.89[EUR][1000 genomes]
rs34409918	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34432857	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34706883	0.92[EUR][1000 genomes]
rs34718920	0.92[EUR][1000 genomes]
rs34788973	0.85[EUR][1000 genomes]
rs35037868	1.00[EUR][1000 genomes]
rs35715914	0.94[EUR][1000 genomes]
rs35819751	0.89[EUR][1000 genomes]
rs36101351	0.85[EUR][1000 genomes]
rs36116761	0.89[EUR][1000 genomes]
rs370155	0.81[EUR][1000 genomes]
rs390764	0.83[EUR][1000 genomes]
rs401754	0.83[EUR][1000 genomes]
rs45509595	0.89[EUR][1000 genomes]
rs56405707	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61742093	0.85[EUR][1000 genomes]
rs66868086	0.89[EUR][1000 genomes]
rs67040724	0.85[EUR][1000 genomes]
rs67101035	0.92[EUR][1000 genomes]
rs67652222	0.92[EUR][1000 genomes]
rs71559038	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71559050	0.92[EUR][1000 genomes]
rs71559054	0.85[EUR][1000 genomes]
rs72845046	0.92[EUR][1000 genomes]
rs72845070	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72847313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9368531	0.83[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35501037	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35501037	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs35501037	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 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	chr6:27730800-27740000	Weak transcription	Primary T cells from cord blood	blood
4	chr6:27737400-27739600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:27738200-27740200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
6	chr6:27738600-27739800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:27738600-27739800	Enhancers	Fetal Intestine Large	intestine
8	chr6:27738600-27741600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:27738800-27740000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
11	chr6:27738800-27740800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr6:27738800-27741800	Enhancers	Primary hematopoietic stem cells	blood
13	chr6:27739000-27739600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:27739000-27739800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:27739000-27739800	Enhancers	Colonic Mucosa	Colon
16	chr6:27739000-27739800	Enhancers	Fetal Intestine Small	intestine
17	chr6:27739000-27739800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:27739000-27740000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:27739000-27740000	Enhancers	K562	blood
20	chr6:27739000-27742000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr6:27739000-27742400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:27739000-27742400	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:27739200-27739600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr6:27739200-27742200	Enhancers	GM12878-XiMat	blood
25	chr6:27739400-27739600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr6:27739400-27739600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr6:27739400-27739600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:27739400-27739600	Enhancers	NHEK	skin
29	chr6:27739400-27739800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr6:27739400-27739800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:27739400-27739800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
32	chr6:27739400-27739800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr6:27739400-27739800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:27739400-27740600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
35	chr6:27739400-27740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:27739400-27741600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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