Variant report

Variant	rs200959
Chromosome Location	chr6:27842047-27842048
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	SPI1	chr6:27841780-27842225	HL-60	blood:	n/a	chr6:27842009-27842022
2	POLR2A	chr6:27837920-27842326	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr6:27840984-27842099	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57920063..57922392-chr6:27841925..27843935,2	MCF-7	breast:
2	chr6:26030829..26032499-chr6:27840625..27843168,2	MCF-7	breast:

Variant related genes	Relation type
HIST1H3I	TF binding region
HIST1H4L	TF binding region
ENSG00000124693	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs149898	0.85[YRI][hapmap]
rs149957	0.82[ASW][hapmap]
rs156741	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs156742	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs16867901	1.00[TSI][hapmap]
rs16867911	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs169263	1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs175597	0.96[MKK][hapmap]
rs187995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200470	1.00[EUR][1000 genomes]
rs200472	1.00[EUR][1000 genomes]
rs200484	0.92[MKK][hapmap]
rs200487	0.84[ASW][hapmap]
rs200501	0.92[MKK][hapmap]
rs200947	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200948	0.96[MKK][hapmap]
rs200955	0.84[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200968	0.81[MKK][hapmap]
rs200970	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs200982	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200984	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200989	0.96[MKK][hapmap]
rs200995	0.81[MKK][hapmap]
rs201003	1.00[EUR][1000 genomes]
rs201005	0.84[ASW][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs2200870	0.83[AMR][1000 genomes]
rs2747054	0.92[MKK][hapmap]
rs276363	1.00[MEX][hapmap]
rs276364	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs276366	0.84[YRI][hapmap]
rs401763	0.84[MKK][hapmap]
rs425159	0.85[YRI][hapmap]
rs55965630	0.83[AMR][1000 genomes]
rs56221999	1.00[AMR][1000 genomes]
rs56262840	1.00[AMR][1000 genomes]
rs56342784	1.00[EUR][1000 genomes]
rs56366090	0.83[AMR][1000 genomes]
rs58700542	1.00[AMR][1000 genomes]
rs59716769	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61275289	0.83[AMR][1000 genomes]
rs73739606	1.00[AMR][1000 genomes]
rs73739685	1.00[AMR][1000 genomes]
rs73739773	0.83[AMR][1000 genomes]
rs73740805	0.83[AMR][1000 genomes]
rs73740842	0.83[AMR][1000 genomes]
rs73742455	1.00[AMR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9295739	1.00[TSI][hapmap]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs200959	SLC5A7	trans	brain	seeQTL
rs200959	LRTM1	trans	brain	seeQTL
rs200959	ASMT	trans	brain	seeQTL
rs200959	OTX2	trans	brain	seeQTL
rs200959	PDE6H	trans	brain	seeQTL
rs200959	CRX	trans	brain	seeQTL
rs200959	GUCA1C	trans	brain	seeQTL
rs200959	SH2D2A	trans	brain	seeQTL
rs200959	Hs.158943	cis	multi-tissue	Pritchard
rs200959	GSG1	trans	brain	seeQTL
rs200959	TTR	trans	brain	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27838600-27842400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr6:27838800-27842400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:27839000-27842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:27839000-27842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:27839000-27842400	Active TSS	Thymus	Thymus
6	chr6:27839000-27842800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:27839200-27842200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:27839800-27842400	Active TSS	Brain Germinal Matrix	brain
9	chr6:27840600-27842400	Flanking Active TSS	Fetal Thymus	thymus
10	chr6:27840800-27842200	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:27841000-27842200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr6:27841200-27842200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:27841200-27842200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr6:27841400-27842200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:27841400-27842200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:27841400-27842400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:27841400-27842400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr6:27841400-27842400	Flanking Active TSS	Dnd41	blood
19	chr6:27841600-27842200	Enhancers	Placenta	Placenta
20	chr6:27841600-27842200	Weak transcription	Gastric	stomach
21	chr6:27841600-27842400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:27841800-27842200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:27841800-27842200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:27841800-27842200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:27841800-27842200	Bivalent Enhancer	Adipose Nuclei	Adipose
26	chr6:27841800-27842200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:27841800-27842200	Enhancers	Fetal Intestine Small	intestine
28	chr6:27841800-27842200	Enhancers	Fetal Muscle Leg	muscle
29	chr6:27841800-27842400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr6:27841800-27842400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr6:27841800-27842400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:27841800-27842600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:27841800-27843800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:27841800-27847000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:27842000-27842200	Enhancers	Primary T cells from cord blood	blood
36	chr6:27842000-27842200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:27842000-27842200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:27842000-27842200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:27842000-27842200	Enhancers	Fetal Stomach	stomach
40	chr6:27842000-27842400	Enhancers	Primary B cells from cord blood	blood
41	chr6:27842000-27842400	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:27842000-27842400	Enhancers	Fetal Muscle Trunk	muscle
43	chr6:27842000-27842600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:27842000-27842600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr6:27842000-27842600	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:27842000-27842600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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