Variant report

Variant	rs34033399
Chromosome Location	chr4:7882215-7882216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7881697..7884478-chr4:7901263..7903029,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11732100	0.89[EUR][1000 genomes]
rs11735005	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130704	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17770213	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17770321	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17832709	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28375300	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28417050	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28437157	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28438948	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28494514	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28544299	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28558196	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28568794	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28600706	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28607519	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28622214	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28694545	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28766602	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34310670	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55844411	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56220381	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56229515	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56411722	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61742221	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62289320	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62289322	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289333	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289335	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289336	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289337	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289338	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289339	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289340	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289359	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62290561	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62290571	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290573	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290574	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290579	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6814219	0.83[EUR][1000 genomes]
rs6814887	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6815298	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6816389	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6829680	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6838073	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6850654	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6855532	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73210862	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210866	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73214041	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214042	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7378072	0.82[EUR][1000 genomes]
rs7663026	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7680747	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7687428	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34033399	AFAP1	cis	Whole Blood	GTEx
rs34033399	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs34033399	AFAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
4	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
6	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
11	chr4:7876800-7885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:7877000-7883200	Enhancers	Colon Smooth Muscle	Colon
13	chr4:7877400-7883200	Enhancers	Fetal Heart	heart
14	chr4:7877400-7885000	Enhancers	NH-A	brain
15	chr4:7877800-7883200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:7877800-7883200	Enhancers	Fetal Stomach	stomach
17	chr4:7877800-7883200	Enhancers	Ovary	ovary
18	chr4:7877800-7883200	Enhancers	HSMM	muscle
19	chr4:7877800-7883400	Enhancers	Fetal Muscle Leg	muscle
20	chr4:7878000-7882400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:7878000-7883000	Enhancers	HSMMtube	muscle
22	chr4:7878000-7883200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:7878200-7882800	Weak transcription	Placenta	Placenta
24	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:7878400-7886600	Weak transcription	Small Intestine	intestine
26	chr4:7878600-7883200	Enhancers	HUVEC	blood vessel
27	chr4:7879000-7888200	Weak transcription	Fetal Intestine Large	intestine
28	chr4:7879200-7882400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:7879400-7882400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:7879400-7883200	Enhancers	Rectal Smooth Muscle	rectum
31	chr4:7879400-7883600	Weak transcription	HMEC	breast
32	chr4:7879400-7888000	Weak transcription	Fetal Brain Female	brain
33	chr4:7879400-7891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:7879600-7882400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr4:7879800-7882400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:7879800-7883200	Enhancers	Left Ventricle	heart
37	chr4:7879800-7886800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:7880000-7882800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr4:7880200-7882400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:7880200-7882600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:7880200-7883000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:7880200-7884800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:7880400-7888000	Weak transcription	Brain Anterior Caudate	brain
44	chr4:7880600-7882800	Enhancers	NHDF-Ad	bronchial
45	chr4:7880600-7883200	Enhancers	NHLF	lung
46	chr4:7880600-7883600	Enhancers	Fetal Muscle Trunk	muscle
47	chr4:7880800-7882600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:7880800-7882600	Enhancers	Fetal Brain Male	brain
49	chr4:7880800-7883200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:7880800-7883200	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links