Variant report

Variant	rs17007139
Chromosome Location	chr1:220293361-220293362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr1:220292107-220293383	HEK293	kidney:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:220292837..220298282-chr1:220298660..220304315,8	K562	blood:
2	chr1:220163115..220165079-chr1:220292412..220294107,2	K562	blood:
3	chr1:220292461..220294314-chr1:220300641..220303068,2	MCF-7	breast:
4	chr1:220286097..220287925-chr1:220293304..220296028,2	K562	blood:
5	chr1:220286097..220288376-chr1:220293126..220296028,3	K562	blood:

No data

Variant related genes	Relation type
MIR215	TF binding region
MIR194-1	TF binding region
ENSG00000067704	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10127631	0.87[GIH][hapmap]
rs1039206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863539	0.87[GIH][hapmap]
rs11118501	0.87[GIH][hapmap]
rs1124763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12031256	0.90[EUR][1000 genomes]
rs12032738	1.00[YRI][hapmap]
rs12037712	0.87[GIH][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12045447	0.83[AFR][1000 genomes]
rs12086760	0.87[GIH][hapmap]
rs1557130	1.00[CEU][hapmap]
rs17007107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17007135	0.85[MKK][hapmap];0.83[YRI][hapmap]
rs34406824	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3767656	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3820455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274792	0.86[ASN][1000 genomes]
rs57463200	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs58256586	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58966246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59935950	0.81[AFR][1000 genomes]
rs60736051	0.85[AFR][1000 genomes]
rs73096563	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73096575	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73096577	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73096595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73098512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098528	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098530	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098537	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098550	0.83[AFR][1000 genomes]
rs73098551	0.83[AFR][1000 genomes]
rs73098553	0.83[AFR][1000 genomes]
rs73098579	0.81[AFR][1000 genomes]
rs874331	1.00[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268400-220293400	Weak transcription	Stomach Mucosa	stomach
2	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:220268600-220293800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:220269200-220293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:220269400-220330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:220270600-220293800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:220278600-220316200	Weak transcription	Pancreas	Pancrea
8	chr1:220281200-220295200	Weak transcription	Right Atrium	heart
9	chr1:220281400-220300600	Weak transcription	NHLF	lung
10	chr1:220281400-220307200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:220281400-220307800	Weak transcription	Psoas Muscle	Psoas
12	chr1:220281400-220314400	Weak transcription	Fetal Brain Male	brain
13	chr1:220284600-220301400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:220284600-220305600	Weak transcription	Small Intestine	intestine
15	chr1:220284600-220307400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:220284600-220307800	Weak transcription	Spleen	Spleen
17	chr1:220284600-220313000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:220284600-220313600	Weak transcription	Gastric	stomach
19	chr1:220284600-220324600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:220284800-220300000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:220284800-220301600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:220285400-220299600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:220288000-220300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:220288200-220324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:220288400-220295200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:220288400-220310200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:220289200-220298600	Weak transcription	Osteobl	bone
28	chr1:220289200-220300000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:220289400-220299000	Weak transcription	GM12878-XiMat	blood
30	chr1:220289400-220301600	Weak transcription	Esophagus	oesophagus
31	chr1:220289600-220297200	Weak transcription	Right Ventricle	heart
32	chr1:220289600-220299000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:220289600-220301400	Weak transcription	Fetal Kidney	kidney
34	chr1:220289600-220301600	Weak transcription	Brain Substantia Nigra	brain
35	chr1:220289600-220307800	Weak transcription	Thymus	Thymus
36	chr1:220289800-220295600	Weak transcription	Brain Anterior Caudate	brain
37	chr1:220289800-220297200	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:220289800-220297800	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:220289800-220299800	Weak transcription	A549	lung
40	chr1:220289800-220300400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:220289800-220300800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:220289800-220301800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:220289800-220306400	Weak transcription	NHEK	skin
44	chr1:220289800-220307400	Weak transcription	HSMMtube	muscle
45	chr1:220289800-220307800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:220290000-220299400	Weak transcription	Fetal Lung	lung
47	chr1:220290000-220299600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:220290200-220300000	Weak transcription	HUVEC	blood vessel
49	chr1:220290200-220300600	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:220290400-220295000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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