Variant report

Variant	rs199741
Chromosome Location	chr6:25931577-25931578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:25931367-25931745	HepG2	liver:	n/a	n/a
2	CUX1	chr6:25931577-25931773	K562	blood:	n/a	n/a
3	CEBPB	chr6:25931376-25931739	K562	blood:	n/a	n/a
4	ARID3A	chr6:25930894-25931730	HepG2	liver:	n/a	n/a
5	ATF1	chr6:25931091-25931738	K562	blood:	n/a	n/a
6	CEBPB	chr6:25931463-25931644	K562	blood:	n/a	n/a
7	CEBPB	chr6:25931389-25931730	IMR90	lung:	n/a	n/a
8	JUND	chr6:25931471-25931711	K562	blood:	n/a	chr6:25931513-25931525
9	CEBPB	chr6:25931413-25931769	MCF-7	breast:	n/a	n/a
10	SPI1	chr6:25931485-25931674	K562	blood:	n/a	n/a
11	CEBPB	chr6:25931385-25931722	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:25931557-25931607	HIPEpiC	eye:	n/a
2	chr6:25931557-25931607	AG10803	skin:	n/a
3	chr6:25931557-25931607	GM12878	blood:	n/a
4	chr6:25931557-25931607	IMR90	lung:	fetal
5	chr6:25931557-25931607	RPTEC	kidney:	n/a
6	chr6:25931557-25931607	AoSMC	blood vessel:	n/a
7	chr6:25931557-25931607	T-47D	breast:	n/a
8	chr6:25931557-25931607	PFSK-1	brain:	n/a
9	chr6:25931557-25931607	NHDF-neo	bronchial:	n/a
10	chr6:25931557-25931607	HUVEC	blood vessel:	n/a
11	chr6:25931557-25931607	GM12891	blood:	n/a
12	chr6:25931557-25931607	Caco-2	colon:	n/a
13	chr6:25931557-25931607	U87	brain:	n/a
14	chr6:25931557-25931607	NB4	blood:	n/a
15	chr6:25931557-25931607	BE2_C	brain:	n/a
16	chr6:25931557-25931607	HCM	heart:	n/a
17	chr6:25931557-25931607	AG04449	skin:	fetal
18	chr6:25931557-25931607	SAEC	small airway:	n/a
19	chr6:25931557-25931607	HMEC	breast:	n/a
20	chr6:25931557-25931607	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:25931557-25931607	HRCEpiC	kidney:	n/a
22	chr6:25931557-25931607	MCF10A-Er-Src	breast:	n/a
23	chr6:25931557-25931607	NHBE	bronchial:	n/a
24	chr6:25931557-25931607	Hepatocyte	liver:	n/a
25	chr6:25931557-25931607	A549	lung:	n/a
26	chr6:25931557-25931607	ECC-1	luminal epithelium:	n/a
27	chr6:25931557-25931607	HAEpiC	amniotic membrane:	n/a
28	chr6:25931557-25931607	K562	blood:	n/a
29	chr6:25931557-25931607	SK-N-MC	brain:	n/a
30	chr6:25931557-25931607	HRE	kidney:	n/a
31	chr6:25931557-25931607	ovcar-3	ovarian:	n/a
32	chr6:25931557-25931607	Jurkat	blood:	n/a
33	chr6:25931557-25931607	NT2-D1	testis:	n/a
34	chr6:25931557-25931607	PrEC	prostate:	n/a
35	chr6:25931557-25931607	AG09309	skin:	n/a
36	chr6:25931557-25931607	MCF-7	breast:	n/a
37	chr6:25931557-25931607	GM19239	blood:	n/a
38	chr6:25931557-25931607	PANC-1	pancreas:	n/a
39	chr6:25931557-25931607	Hela-S3	cervix:	n/a
40	chr6:25931557-25931607	CMK	blood:	n/a
41	chr6:25931557-25931607	HEK293	kidney:	embryo
42	chr6:25931557-25931607	BJ	skin:	n/a
43	chr6:25931557-25931607	SK-N-SH_RA	brain:	n/a
44	chr6:25931557-25931607	LNCaP	prostate:	n/a
45	chr6:25931557-25931607	HCF	heart:	n/a
46	chr6:25931557-25931607	HCPEpiC	choroid plexus:	n/a
47	chr6:25931557-25931607	HCT-116	colon:	n/a
48	chr6:25931557-25931607	SKMC	muscle:	n/a
49	chr6:25931557-25931607	HNPCEpiC	eye:	n/a
50	chr6:25931557-25931607	GM06990	blood:	n/a

No data

Variant related genes	Relation type
SLC17A2	TF binding region
SLC17A2	CpG island

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10425	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[LWK][hapmap]
rs115810	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1165170	0.82[ASN][1000 genomes]
rs1165172	0.82[ASN][1000 genomes]
rs1165201	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12346	0.83[CHD][hapmap]
rs129129	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1540275	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs1540276	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs169219	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs175319	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs198810	0.86[CHB][hapmap]
rs198815	0.86[CHB][hapmap]
rs198820	0.86[CHB][hapmap]
rs198845	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs198848	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs198852	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs198853	0.86[CHB][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap]
rs199725	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199726	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199734	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199736	0.89[ASN][1000 genomes]
rs199737	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199739	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs199743	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199747	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs199748	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs199750	0.84[ASW][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs199751	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs199752	0.84[ASW][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs199753	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs199754	0.84[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs199755	0.86[AMR][1000 genomes]
rs2032447	0.86[CHB][hapmap]
rs2051540	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2213284	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs2230655	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs3903852	0.86[JPT][hapmap]
rs428469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4401650	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs442601	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs473913	0.82[ASN][1000 genomes]
rs478349	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483906	0.82[ASN][1000 genomes]
rs517842	0.83[ASN][1000 genomes]
rs518700	0.83[ASN][1000 genomes]
rs531750	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs537581	0.84[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.82[ASN][1000 genomes]
rs599444	0.84[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.82[ASN][1000 genomes]
rs629835	1.00[JPT][hapmap]
rs645279	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6901039	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs6922788	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs7756117	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs7767546	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs807212	1.00[CHB][hapmap]
rs807214	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs9379811	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9467664	0.86[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv5229	chr6:25912151-25956558	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs199741	HIST1H2AJ	cis	parietal	SCAN
rs199741	HIST1H2BI	cis	cerebellum	SCAN
rs199741	ZNF323	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25928400-25934400	Weak transcription	Small Intestine	intestine
2	chr6:25929000-25931600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:25929800-25934400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:25930800-25933800	Enhancers	HepG2	liver
5	chr6:25931000-25931600	Enhancers	Fetal Intestine Small	intestine
6	chr6:25931400-25931800	Active TSS	Liver	Liver

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