Variant report

Variant	rs885655
Chromosome Location	chr21:46181679-46181680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46038244..46039107-chr21:46180990..46181837,2	MCF-7	breast:
2	chr21:46180771..46183502-chr21:46265966..46267491,2	MCF-7	breast:
3	chr21:46179049..46181876-chr21:46183341..46186313,2	K562	blood:
4	chr21:46171917..46177806-chr21:46181342..46188371,13	MCF-7	breast:
5	chr21:46179049..46181876-chr21:46183341..46186313,3	K562	blood:
6	chr21:46181402..46184380-chr21:46359332..46361437,2	K562	blood:
7	chr21:46175791..46179741-chr21:46180006..46182976,4	K562	blood:

Variant related genes	Relation type
ENSG00000160256	Chromatin interaction
ENSG00000183250	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1071792	0.81[EUR][1000 genomes]
rs1109280	0.84[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs11702064	0.85[CHD][hapmap]
rs1347324	0.84[EUR][1000 genomes]
rs1821431	0.85[EUR][1000 genomes]
rs2294157	0.85[EUR][1000 genomes]
rs2329899	0.84[EUR][1000 genomes]
rs2329900	0.84[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2838673	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838674	1.00[ASN][1000 genomes]
rs2838675	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838678	0.85[EUR][1000 genomes]
rs2838686	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2838699	0.92[CHD][hapmap]
rs3788136	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs4239838	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4818973	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818974	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818975	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs55659309	1.00[ASN][1000 genomes]
rs62222752	0.80[EUR][1000 genomes]
rs6518204	0.85[CHD][hapmap]
rs733161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs760431	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs8103	0.84[CEU][hapmap];0.92[CHD][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs8128992	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs885656	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];1.00[ASN][1000 genomes]
rs885657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs885655	C21orf58	cis	parietal	SCAN
rs885655	RIPK4	cis	cerebellum	SCAN
rs885655	PTTG1IP	cis	multi-tissue	Pritchard
rs885655	NCRNA00175	cis	parietal	SCAN
rs885655	PTTG1IP	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46168000-46185800	Weak transcription	Right Atrium	heart
2	chr21:46171400-46183400	Weak transcription	Gastric	stomach
3	chr21:46179000-46183400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:46179600-46184600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:46179800-46182000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr21:46180000-46181800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr21:46180400-46182000	Enhancers	Fetal Muscle Leg	muscle
8	chr21:46180400-46182600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr21:46180600-46181800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:46180800-46181800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr21:46180800-46183400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:46180800-46184800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr21:46181200-46188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr21:46181400-46181800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr21:46181400-46183000	Flanking Active TSS	HepG2	liver
16	chr21:46181600-46181800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr21:46181600-46181800	Enhancers	Duodenum Mucosa	Duodenum
18	chr21:46181600-46181800	Enhancers	Fetal Intestine Small	intestine
19	chr21:46181600-46181800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
20	chr21:46181600-46181800	Active TSS	Rectal Smooth Muscle	rectum
21	chr21:46181600-46181800	Enhancers	HMEC	breast
22	chr21:46181600-46181800	Enhancers	K562	blood
23	chr21:46181600-46181800	Flanking Active TSS	NHEK	skin
24	chr21:46181600-46182000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr21:46181600-46182000	Enhancers	Colonic Mucosa	Colon
26	chr21:46181600-46182000	Enhancers	Esophagus	oesophagus
27	chr21:46181600-46182000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr21:46181600-46182000	Enhancers	Stomach Mucosa	stomach
29	chr21:46181600-46182200	Enhancers	Fetal Intestine Large	intestine
30	chr21:46181600-46182400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr21:46181600-46184800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr21:46181600-46185000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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