Variant report

Variant	rs16998550
Chromosome Location	chr21:41170253-41170254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:41169026..41172002-chr21:41176222..41177881,2	MCF-7	breast:
2	chr21:41165014..41167471-chr21:41168661..41171078,3	MCF-7	breast:
3	chr21:41162459..41164745-chr21:41169799..41171557,2	K562	blood:

Variant related genes	Relation type
ENSG00000183067	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs16998420	1.00[CEU][hapmap]
rs16998436	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16998444	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16998490	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998519	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998521	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16998532	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16998534	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998553	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998556	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998576	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17753538	0.96[EUR][1000 genomes]
rs1888493	1.00[CEU][hapmap]
rs2205202	1.00[CEU][hapmap]
rs2837204	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs455712	0.82[JPT][hapmap]
rs456303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs456412	0.82[JPT][hapmap]
rs456800	0.82[JPT][hapmap]
rs460504	0.81[JPT][hapmap]
rs460604	0.82[JPT][hapmap]
rs465343	0.82[JPT][hapmap]
rs465958	0.82[JPT][hapmap]
rs466577	0.82[JPT][hapmap]
rs55739464	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56955296	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67969662	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7277040	0.82[JPT][hapmap]
rs73215346	0.94[EUR][1000 genomes]
rs73217283	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73217284	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73217286	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73217292	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73217299	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73217300	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73219407	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73219481	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73219482	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73219485	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73219486	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73219489	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73219490	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73219491	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73221250	0.94[EUR][1000 genomes]
rs73904413	0.96[ASN][1000 genomes]
rs73904418	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73904443	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127368	0.92[EUR][1000 genomes];0.93[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	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers 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	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834099	chr21:41076873-41206030	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41161000-41171000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:41161400-41170400	Weak transcription	Right Atrium	heart
3	chr21:41161400-41180000	Weak transcription	Pancreas	Pancrea
4	chr21:41163600-41170400	Weak transcription	Fetal Heart	heart
5	chr21:41164200-41185600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:41166200-41173200	Weak transcription	Placenta	Placenta
7	chr21:41168400-41170800	Weak transcription	Right Ventricle	heart
8	chr21:41168800-41170600	Weak transcription	Fetal Brain Male	brain
9	chr21:41170000-41171200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr21:41170200-41170400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:41170200-41171000	Enhancers	Left Ventricle	heart
12	chr21:41170200-41171400	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links