Variant report

Variant	rs895675
Chromosome Location	chr6:25036497-25036498
allele	A/G
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	ATF1	chr6:25036233-25036616	K562	blood:	n/a	n/a
2	GATA2	chr6:25036198-25036585	K562	blood:	n/a	n/a
3	GATA3	chr6:25036091-25036781	SK-N-SH	brain:	n/a	n/a
4	MAFK	chr6:25036214-25036668	K562	blood:	n/a	chr6:25036424-25036439
5	SPI1	chr6:25036270-25036497	GM12878	blood:	n/a	n/a
6	JUND	chr6:25036177-25036663	K562	blood:	n/a	chr6:25036364-25036375 chr6:25036367-25036377 chr6:25036538-25036547
7	GATA1	chr6:25035578-25036794	K562	blood:	n/a	chr6:25035907-25035916 chr6:25036078-25036089
8	TEAD4	chr6:25036227-25036653	K562	blood:	n/a	n/a
9	MYC	chr6:25036135-25036651	K562	blood:	n/a	n/a
10	TBL1XR1	chr6:25036298-25036635	K562	blood:	n/a	n/a
11	GATA1	chr6:25036274-25036651	K562	blood:	n/a	n/a
12	RUNX3	chr6:25036108-25036629	GM12878	blood:	n/a	n/a
13	BHLHE40	chr6:25035572-25036590	GM12878	blood:	n/a	n/a
14	GATA2	chr6:25036286-25036675	K562	blood:	n/a	n/a
15	SPI1	chr6:25036251-25036583	K562	blood:	n/a	n/a
16	SPI1	chr6:25036171-25036651	HL-60	blood:	n/a	n/a
17	BACH1	chr6:25036260-25036670	K562	blood:	n/a	n/a
18	GATA1	chr6:25036210-25036668	PBDEFetal	blood:	n/a	n/a
19	MAFF	chr6:25036275-25036679	K562	blood:	n/a	n/a
20	BHLHE40	chr6:25035708-25036602	K562	blood:	n/a	n/a
21	TAL1	chr6:25036275-25036630	K562	blood:	n/a	n/a
22	RCOR1	chr6:25035779-25036719	K562	blood:	n/a	n/a
23	NFIC	chr6:25036168-25036647	GM12878	blood:	n/a	n/a
24	SPI1	chr6:25036281-25036580	GM12891	blood:	n/a	n/a
25	ZMIZ1	chr6:25036281-25036645	K562	blood:	n/a	n/a
26	RUNX3	chr6:25035565-25036538	GM12878	blood:	n/a	n/a
27	MAX	chr6:25036259-25036579	K562	blood:	n/a	n/a
28	HMGN3	chr6:25036271-25036594	K562	blood:	n/a	n/a
29	SPI1	chr6:25036265-25036560	K562	blood:	n/a	n/a
30	GATA3	chr6:25036172-25036763	MCF-7	breast:	n/a	n/a
31	POLR2A	chr6:25034725-25036865	PBDE	blood:	n/a	n/a
32	GATA2	chr6:25036264-25036653	K562	blood:	n/a	n/a
33	GATA1	chr6:25035662-25037146	PBDE	blood:	n/a	chr6:25035907-25035916 chr6:25036078-25036089
34	PML	chr6:25036274-25036626	K562	blood:	n/a	n/a
35	CEBPD	chr6:25036180-25036747	K562	blood:	n/a	n/a
36	MYC	chr6:25035946-25036598	K562	blood:	n/a	n/a
37	RCOR1	chr6:25036289-25036642	K562	blood:	n/a	n/a
38	CCNT2	chr6:25036286-25036625	K562	blood:	n/a	n/a
39	GATA3	chr6:25036094-25036690	SK-N-SH	brain:	n/a	n/a
40	TEAD4	chr6:25036109-25036732	K562	blood:	n/a	n/a
41	EP300	chr6:25036269-25036687	K562	blood:	n/a	n/a
42	WRNIP1	chr6:25035376-25036566	GM12878	blood:	n/a	n/a
43	MAZ	chr6:25036215-25036570	K562	blood:	n/a	n/a
44	PAX5	chr6:25036184-25036532	GM12878	blood:	n/a	chr6:25036381-25036399
45	CBX3	chr6:25036231-25036613	K562	blood:	n/a	n/a
46	JUN	chr6:25036277-25036629	K562	blood:	n/a	chr6:25036364-25036375 chr6:25036367-25036377 chr6:25036538-25036547
47	CEBPD	chr6:25036188-25036722	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25032692..25035035-chr6:25036206..25038734,3	K562	blood:
2	chr6:25028396..25029900-chr6:25034648..25037120,2	K562	blood:
3	chr6:24895729..24898166-chr6:25036279..25038018,2	K562	blood:

Variant related genes	Relation type
RN7SL334P	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1046142	0.87[EUR][1000 genomes]
rs1128826	0.87[EUR][1000 genomes]
rs1128827	0.87[EUR][1000 genomes]
rs11963128	0.87[EUR][1000 genomes]
rs11965266	0.87[EUR][1000 genomes]
rs12333217	0.87[EUR][1000 genomes]
rs12333219	0.87[EUR][1000 genomes]
rs12333222	0.87[EUR][1000 genomes]
rs12333327	0.87[EUR][1000 genomes]
rs160035	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890032	0.87[EUR][1000 genomes]
rs16890067	0.87[EUR][1000 genomes]
rs16890087	0.87[EUR][1000 genomes]
rs16890100	0.87[EUR][1000 genomes]
rs2394361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516576	0.85[EUR][1000 genomes]
rs4538700	0.87[EUR][1000 genomes]
rs6456648	0.87[EUR][1000 genomes]
rs6905460	0.87[EUR][1000 genomes]
rs6905554	0.85[EUR][1000 genomes]
rs6905624	0.87[EUR][1000 genomes]
rs6906421	0.85[EUR][1000 genomes]
rs6913324	0.87[EUR][1000 genomes]
rs6915329	0.87[EUR][1000 genomes]
rs6925889	0.87[EUR][1000 genomes]
rs733535	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740848	0.87[EUR][1000 genomes]
rs7745550	0.87[EUR][1000 genomes]
rs7745609	0.87[EUR][1000 genomes]
rs7756507	0.87[EUR][1000 genomes]
rs7762804	0.85[EUR][1000 genomes]
rs7773107	0.87[EUR][1000 genomes]
rs7774557	0.87[EUR][1000 genomes]
rs895674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916537	0.85[EUR][1000 genomes]
rs916538	0.85[EUR][1000 genomes]
rs916539	0.85[EUR][1000 genomes]
rs9461096	0.87[EUR][1000 genomes]
rs9461101	0.87[EUR][1000 genomes]
rs9461104	0.85[EUR][1000 genomes]
rs9467394	0.87[EUR][1000 genomes]
rs9467395	0.87[EUR][1000 genomes]
rs9467396	0.87[EUR][1000 genomes]
rs9467397	0.85[EUR][1000 genomes]
rs9467398	0.87[EUR][1000 genomes]
rs9467399	0.87[EUR][1000 genomes]
rs9467400	0.87[EUR][1000 genomes]
rs9467401	0.87[EUR][1000 genomes]
rs9467403	0.87[EUR][1000 genomes]
rs9467404	0.87[EUR][1000 genomes]
rs9467405	0.87[EUR][1000 genomes]
rs9467406	0.87[EUR][1000 genomes]
rs9467408	0.87[EUR][1000 genomes]
rs9467409	0.87[EUR][1000 genomes]
rs9467410	0.85[EUR][1000 genomes]
rs9467411	0.85[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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs895675	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25028200-25037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25034600-25036600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:25034600-25036600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr6:25034600-25036600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr6:25034600-25036600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:25034600-25036600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:25034600-25036600	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:25034600-25036800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr6:25034600-25036800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr6:25034600-25036800	Flanking Active TSS	Dnd41	blood
11	chr6:25034600-25037200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:25034600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:25034800-25037200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:25035000-25036600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr6:25035000-25037000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:25035000-25037400	Enhancers	K562	blood
17	chr6:25035200-25036600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr6:25035200-25036600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr6:25035200-25041200	Weak transcription	Fetal Kidney	kidney
20	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
21	chr6:25035400-25036600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:25035600-25036600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:25035600-25037200	Enhancers	Placenta	Placenta
24	chr6:25035800-25036600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr6:25035800-25037800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:25035800-25039400	Weak transcription	Liver	Liver
27	chr6:25035800-25040600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:25035800-25041000	Enhancers	Fetal Thymus	thymus
29	chr6:25036000-25038800	Weak transcription	Spleen	Spleen
30	chr6:25036000-25042400	Weak transcription	Lung	lung
31	chr6:25036200-25036600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:25036200-25036600	Enhancers	NH-A	brain
33	chr6:25036400-25036600	Enhancers	Primary T cells from cord blood	blood
34	chr6:25036400-25036600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr6:25036400-25036800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:25036400-25037000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:25036400-25037000	Enhancers	Primary B cells from cord blood	blood
38	chr6:25036400-25037600	Enhancers	Thymus	Thymus
39	chr6:25036400-25038000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:25036400-25038000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:25036400-25038600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr6:25036400-25039000	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:25036400-25040600	Enhancers	Primary B cells from peripheral blood	blood
44	chr6:25036400-25041000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:25036400-25041000	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links