Variant report

Variant	rs34105070
Chromosome Location	chr6:27560805-27560806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:180)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:180 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:27560222-27560889	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr6:27560261-27560914	K562	blood:	n/a	n/a
3	PML	chr6:27560120-27561014	GM12878	blood:	n/a	n/a
4	EP300	chr6:27560292-27560837	GM12878	blood:	n/a	n/a
5	TEAD4	chr6:27560254-27560936	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr6:27560485-27560814	GM12878	blood:	n/a	n/a
7	FOSL2	chr6:27560370-27560833	HepG2	liver:	n/a	n/a
8	ELF1	chr6:27560361-27560819	HepG2	liver:	n/a	n/a
9	FOXA2	chr6:27560359-27560850	HepG2	liver:	n/a	n/a
10	BHLHE40	chr6:27560016-27560994	K562	blood:	n/a	n/a
11	REST	chr6:27560076-27560941	K562	blood:	n/a	n/a
12	POLR2A	chr6:27559682-27561420	H1-neurons	neurons:	n/a	n/a
13	REST	chr6:27560462-27560862	HL-60	blood:	n/a	n/a
14	RUNX3	chr6:27560261-27560834	GM12878	blood:	n/a	n/a
15	RPC155	chr6:27560186-27560885	Hela-S3	cervix:	n/a	n/a
16	SIN3A	chr6:27559517-27561282	H1-hESC	embryonic stem cell:	n/a	chr6:27561096-27561109
17	REST	chr6:27560418-27560924	HepG2	liver:	n/a	n/a
18	REST	chr6:27560505-27560925	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr6:27560513-27560846	A549	lung:	n/a	n/a
20	MYC	chr6:27560366-27560845	K562	blood:	n/a	n/a
21	JUN	chr6:27560134-27560870	K562	blood:	n/a	n/a
22	SIN3AK20	chr6:27560472-27560849	H1-hESC	embryonic stem cell:	n/a	n/a
23	BRCA1	chr6:27560404-27560971	H1-hESC	embryonic stem cell:	n/a	n/a
24	ETS1	chr6:27560388-27560842	A549	lung:	n/a	chr6:27560437-27560444
25	REST	chr6:27560282-27561113	A549	lung:	n/a	chr6:27561096-27561105
26	MAX	chr6:27560287-27560870	K562	blood:	n/a	n/a
27	CCNT2	chr6:27560140-27560939	K562	blood:	n/a	chr6:27560689-27560709
28	TCF12	chr6:27560510-27560827	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr6:27560446-27560931	H1-hESC	embryonic stem cell:	n/a	n/a
30	SMC3	chr6:27560378-27560973	HepG2	liver:	n/a	n/a
31	ATF3	chr6:27559169-27561107	A549	lung:	n/a	n/a
32	ATF3	chr6:27560301-27560980	HCT-116	colon:	n/a	n/a
33	REST	chr6:27560418-27560863	GM12878	blood:	n/a	n/a
34	REST	chr6:27560543-27560833	Hela-S3	cervix:	n/a	n/a
35	REST	chr6:27560178-27561082	PFSK-1	brain:	n/a	n/a
36	BCLAF1	chr6:27560119-27560892	K562	blood:	n/a	n/a
37	STAT5A	chr6:27560030-27560946	GM12878	blood:	n/a	chr6:27560187-27560196 chr6:27560188-27560197 chr6:27560188-27560211 chr6:27560185-27560199
38	MAX	chr6:27560125-27560840	ECC-1	luminal epithelium:	n/a	n/a
39	REST	chr6:27560472-27560892	PANC-1	pancreas:	n/a	n/a
40	CEBPB	chr6:27560254-27560951	GM12878	blood:	n/a	n/a
41	ELF1	chr6:27560491-27560846	GM12878	blood:	n/a	n/a
42	TEAD4	chr6:27560237-27561012	HepG2	liver:	n/a	n/a
43	MYBL2	chr6:27560146-27561069	HepG2	liver:	n/a	n/a
44	ARID3A	chr6:27560409-27560865	HepG2	liver:	n/a	n/a
45	HDAC2	chr6:27560332-27560812	K562	blood:	n/a	chr6:27560747-27560761 chr6:27560746-27560760 chr6:27560690-27560699
46	FOSL2	chr6:27560339-27560936	SK-N-SH	brain:	n/a	n/a
47	SP1	chr6:27560409-27560834	GM12878	blood:	n/a	n/a
48	NFIC	chr6:27560167-27560909	GM12878	blood:	n/a	n/a
49	GATA2	chr6:27560258-27561005	K562	blood:	n/a	chr6:27560691-27560698 chr6:27560690-27560700 chr6:27560688-27560698 chr6:27560686-27560700 chr6:27560691-27560700
50	MAX	chr6:27560330-27560857	Hela-S3	cervix:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27558513..27562026-chr6:27562388..27564787,3	K562	blood:
2	chr6:27485761..27488358-chr6:27559045..27561077,2	K562	blood:
3	chr6:27531650..27535233-chr6:27560375..27562860,3	K562	blood:
4	chr6:27532623..27535233-chr6:27560375..27562747,2	K562	blood:
5	chr6:27516649..27519121-chr6:27558606..27561383,2	K562	blood:
6	chr6:27549818..27556949-chr6:27557615..27563432,7	K562	blood:
7	chr6:27549715..27554180-chr6:27555593..27563261,8	K562	blood:
8	chr6:27560791..27564329-chr6:27775763..27778725,3	K562	blood:
9	chr6:27560152..27562900-chr6:28715549..28717321,2	K562	blood:
10	chr6:27558583..27561214-chr6:27719565..27721812,2	K562	blood:
11	chr6:27559085..27561066-chr6:27755940..27758239,2	K562	blood:
12	chr6:27558513..27561961-chr6:27562522..27566444,4	K562	blood:
13	chr6:27513701..27516143-chr6:27559137..27561028,2	K562	blood:

No data

Variant related genes	Relation type
RNU6-471P	TF binding region
ENSG00000196747	Chromatin interaction
ENSG00000206671	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10484399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13191474	0.83[EUR][1000 genomes]
rs13192965	0.92[EUR][1000 genomes]
rs13193480	0.87[EUR][1000 genomes]
rs13193542	0.87[EUR][1000 genomes]
rs13195040	0.83[EUR][1000 genomes]
rs13195636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13201294	0.81[EUR][1000 genomes]
rs13202291	0.85[EUR][1000 genomes]
rs13202295	0.87[EUR][1000 genomes]
rs13202775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13209332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13210634	0.92[EUR][1000 genomes]
rs13212318	0.91[EUR][1000 genomes]
rs13215275	0.92[EUR][1000 genomes]
rs13217620	0.92[EUR][1000 genomes]
rs17749927	0.92[EUR][1000 genomes]
rs17750747	0.87[EUR][1000 genomes]
rs34064842	0.91[EUR][1000 genomes]
rs34196306	0.83[EUR][1000 genomes]
rs34409918	0.91[EUR][1000 genomes]
rs34432857	0.91[EUR][1000 genomes]
rs34573979	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34613987	0.82[EUR][1000 genomes]
rs34864796	0.82[EUR][1000 genomes]
rs34965299	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35037868	0.87[EUR][1000 genomes]
rs35501037	0.87[EUR][1000 genomes]
rs35715914	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35848276	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41269265	0.83[EUR][1000 genomes]
rs56405707	0.92[EUR][1000 genomes]
rs58616630	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs66785117	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67240003	0.82[EUR][1000 genomes]
rs67652222	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6904596	0.82[EUR][1000 genomes]
rs6918792	0.81[EUR][1000 genomes]
rs71559038	0.91[EUR][1000 genomes]
rs72845046	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72845070	0.92[EUR][1000 genomes]
rs72847313	0.87[EUR][1000 genomes]
rs7749305	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34105070	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs34105070	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34105070	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27559400-27561000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27559400-27561200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:27559400-27561200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:27559600-27561000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:27559600-27561000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:27559600-27561000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:27559600-27561000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr6:27559600-27561000	Active TSS	NH-A	brain
9	chr6:27559600-27561200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:27559600-27561400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:27559600-27561400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:27559600-27561400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:27559600-27561600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr6:27559600-27561600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:27559600-27561800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:27559600-27562000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:27559600-27562200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:27559600-27562200	Active TSS	A549	lung
19	chr6:27559600-27562600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:27559600-27562800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:27559800-27561000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:27559800-27561000	Active TSS	NHDF-Ad	bronchial
23	chr6:27559800-27561200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
24	chr6:27559800-27561200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr6:27559800-27561400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:27559800-27561400	Active TSS	Muscle Satellite Cultured Cells	--
27	chr6:27559800-27561400	Bivalent Enhancer	Fetal Intestine Large	intestine
28	chr6:27559800-27561400	Active TSS	NHLF	lung
29	chr6:27559800-27561600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:27559800-27561800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:27559800-27562000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr6:27560000-27561000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr6:27560000-27561000	Active TSS	HSMM	muscle
34	chr6:27560000-27561200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:27560000-27561200	Bivalent/Poised TSS	HepG2	liver
36	chr6:27560000-27561400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr6:27560200-27561000	Active TSS	Hela-S3	cervix
38	chr6:27560200-27561200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
39	chr6:27560200-27561200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:27560400-27561000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:27560400-27561000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
42	chr6:27560600-27561000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:27560600-27561000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:27560600-27561000	Bivalent Enhancer	Fetal Stomach	stomach
45	chr6:27560600-27561200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
46	chr6:27560600-27561400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:27560600-27561400	Flanking Active TSS	NHEK	skin
48	chr6:27560600-27561600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:27560800-27561000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
50	chr6:27560800-27561000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood

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