Variant report

Variant	rs11554621
Chromosome Location	chr16:74750396-74750397
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	chr16:74732966..74736026-chr16:74749843..74752746,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168404	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11554620	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34089769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34130324	0.82[EUR][1000 genomes]
rs34219496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34398985	0.81[EUR][1000 genomes]
rs34937987	0.82[EUR][1000 genomes]
rs35038783	0.81[EUR][1000 genomes]
rs35173843	0.82[EUR][1000 genomes]
rs35937344	0.82[EUR][1000 genomes]
rs56664536	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs57844314	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6564160	0.95[ASN][1000 genomes]
rs6564161	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71392613	0.82[EUR][1000 genomes]
rs71392614	0.82[EUR][1000 genomes]
rs71392615	0.81[EUR][1000 genomes]
rs7190389	0.95[ASN][1000 genomes]
rs7191746	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7192122	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7192551	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7193407	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73614642	0.95[ASN][1000 genomes]
rs73614655	0.90[ASN][1000 genomes]
rs73614659	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73614660	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73614661	0.90[ASN][1000 genomes]
rs8047410	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv906907	chr16:74702254-74785902	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv517513	chr16:74743736-74812676	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74735000-74760000	Weak transcription	Esophagus	oesophagus
2	chr16:74743800-74759000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr16:74743800-74759400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr16:74743800-74760800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:74744000-74752400	Weak transcription	Thymus	Thymus
6	chr16:74744000-74760600	Weak transcription	Hela-S3	cervix
7	chr16:74744000-74760800	Weak transcription	Stomach Mucosa	stomach
8	chr16:74744000-74760800	Weak transcription	A549	lung
9	chr16:74744200-74758200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:74747200-74752000	Weak transcription	Fetal Thymus	thymus
11	chr16:74747400-74751800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr16:74747400-74753000	Strong transcription	Fetal Intestine Small	intestine
13	chr16:74748000-74750400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:74748000-74750800	Weak transcription	Brain Angular Gyrus	brain
15	chr16:74748000-74750800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr16:74748200-74758400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr16:74748400-74758200	Weak transcription	Gastric	stomach
18	chr16:74748600-74750400	Weak transcription	Fetal Stomach	stomach
19	chr16:74748600-74750600	Weak transcription	Brain Substantia Nigra	brain
20	chr16:74748600-74751000	Weak transcription	Brain Hippocampus Middle	brain
21	chr16:74748600-74751200	Weak transcription	Brain Anterior Caudate	brain
22	chr16:74748800-74750800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr16:74749000-74758200	Weak transcription	Colonic Mucosa	Colon
24	chr16:74750200-74750400	Active TSS	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links