Variant report

Variant	rs4656349
Chromosome Location	chr1:162049824-162049825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:162038710..162042512-chr1:162047887..162051244,6	MCF-7	breast:
2	chr1:162047961..162049693-chr1:162049742..162052410,2	K562	blood:

Variant related genes	Relation type
ENSG00000198929	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10157090	0.85[ASN][1000 genomes]
rs10159401	0.85[ASN][1000 genomes]
rs10458387	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10458392	0.83[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10737536	0.82[ASN][1000 genomes]
rs10753746	0.82[MEX][hapmap]
rs10753754	0.81[AMR][1000 genomes]
rs10753762	0.86[ASN][1000 genomes]
rs10800279	0.82[MEX][hapmap]
rs10800298	0.81[AMR][1000 genomes]
rs10800303	0.81[AMR][1000 genomes]
rs10800305	0.81[AMR][1000 genomes]
rs10800307	0.82[ASN][1000 genomes]
rs10800311	0.81[AMR][1000 genomes]
rs10918615	0.93[ASN][1000 genomes]
rs10918630	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918671	0.81[AMR][1000 genomes]
rs10918680	0.82[AMR][1000 genomes]
rs10918684	0.81[AMR][1000 genomes]
rs10918687	0.81[AMR][1000 genomes]
rs10918688	0.81[AMR][1000 genomes]
rs1123015	0.81[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11579080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022557	0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs12023182	0.93[ASN][1000 genomes]
rs12044487	0.82[MEX][hapmap]
rs12090585	0.82[MEX][hapmap]
rs12096347	0.80[ASN][1000 genomes]
rs12404369	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12406785	0.81[AMR][1000 genomes]
rs12407513	0.81[AMR][1000 genomes]
rs12567211	0.86[MEX][hapmap]
rs12727141	0.81[AMR][1000 genomes]
rs12727810	0.81[AMR][1000 genomes]
rs1337060	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1337061	0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1337062	0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1415256	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1415257	0.81[AMR][1000 genomes]
rs1415260	0.81[AMR][1000 genomes]
rs1415262	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1415264	0.86[ASN][1000 genomes]
rs1415265	0.86[ASN][1000 genomes]
rs2095626	0.81[AMR][1000 genomes]
rs2210942	0.81[AMR][1000 genomes]
rs2225847	0.82[ASN][1000 genomes]
rs34578934	0.89[ASN][1000 genomes]
rs35021332	0.93[ASN][1000 genomes]
rs3922867	0.81[AMR][1000 genomes]
rs4098274	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233385	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs4656348	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656350	0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4656352	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657140	0.81[AMR][1000 genomes]
rs4657141	0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657142	0.81[AMR][1000 genomes]
rs4657143	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657145	0.81[AMR][1000 genomes]
rs4657152	0.86[ASN][1000 genomes]
rs4657154	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4657155	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs5000342	0.87[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427650	0.85[ASN][1000 genomes]
rs6427651	0.85[ASN][1000 genomes]
rs6660701	0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6664115	0.86[ASN][1000 genomes]
rs6670339	0.81[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6672881	0.81[AMR][1000 genomes]
rs6684179	0.86[ASN][1000 genomes]
rs6684278	0.85[ASN][1000 genomes]
rs6688966	0.81[AMR][1000 genomes]
rs6696160	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6702936	0.82[MEX][hapmap]
rs7417931	0.81[AMR][1000 genomes]
rs7512106	0.82[JPT][hapmap]
rs7514962	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7515045	0.87[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7534045	0.85[ASN][1000 genomes]
rs7538490	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7540690	0.81[CHD][hapmap]
rs7541332	0.81[AMR][1000 genomes]
rs7548348	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs945706	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][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	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1821140	chr1:162047541-162389040	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:162041200-162050200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:162041400-162063600	Weak transcription	Fetal Stomach	stomach
3	chr1:162042400-162050200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:162042600-162050400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:162042600-162051000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:162042600-162052000	Weak transcription	Fetal Kidney	kidney
7	chr1:162044800-162050200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:162044800-162050400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:162044800-162056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:162045000-162050200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:162045000-162056200	Weak transcription	Liver	Liver
12	chr1:162046000-162050800	Weak transcription	HepG2	liver
13	chr1:162046800-162051200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:162047600-162050600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:162047800-162050200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:162047800-162050400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:162047800-162051000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:162048000-162050000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:162048000-162050200	Weak transcription	Right Atrium	heart
20	chr1:162048000-162050400	Weak transcription	Right Ventricle	heart
21	chr1:162048000-162050800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:162048000-162051000	Weak transcription	Pancreas	Pancrea
23	chr1:162048000-162051000	Weak transcription	Stomach Mucosa	stomach
24	chr1:162048000-162051200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:162048000-162055600	Weak transcription	Aorta	Aorta
26	chr1:162048000-162056800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:162048400-162050200	Weak transcription	Gastric	stomach
28	chr1:162048600-162050600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:162048600-162051400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:162048800-162051400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:162048800-162058400	Weak transcription	Left Ventricle	heart
32	chr1:162048800-162061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:162049000-162051200	Enhancers	Fetal Brain Female	brain
34	chr1:162049200-162050400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr1:162049200-162050400	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:162049200-162051200	Enhancers	Colon Smooth Muscle	Colon
37	chr1:162049400-162050000	Weak transcription	Brain Substantia Nigra	brain
38	chr1:162049400-162050800	Enhancers	Hela-S3	cervix
39	chr1:162049600-162050000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:162049600-162050800	Enhancers	Fetal Brain Male	brain
41	chr1:162049800-162050200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:162049800-162053600	Weak transcription	Fetal Heart	heart
43	chr1:162049800-162056800	Weak transcription	H1 Cell Line	embryonic stem cell

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