Variant report

Variant	rs6839119
Chromosome Location	chr4:7918166-7918167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10938695	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12641498	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs13115283	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs13127935	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13139805	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1320074	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1320075	0.83[EUR][1000 genomes]
rs16841407	0.84[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17770447	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17833038	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1878325	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2385910	0.81[EUR][1000 genomes]
rs28500712	0.82[ASN][1000 genomes]
rs28681260	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34179701	0.84[EUR][1000 genomes]
rs4549363	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4696746	0.83[EUR][1000 genomes]
rs4696778	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4696779	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs57831033	0.83[EUR][1000 genomes]
rs59521811	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6811851	0.82[EUR][1000 genomes]
rs6824410	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824700	0.90[JPT][hapmap]
rs6831381	0.82[ASN][1000 genomes]
rs6844956	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845653	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6846317	0.84[EUR][1000 genomes]
rs6848540	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6857814	0.82[EUR][1000 genomes]
rs7694650	0.83[EUR][1000 genomes]
rs938604	0.84[CEU][hapmap];0.83[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6839119	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
3	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
4	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
5	chr4:7912800-7931200	Weak transcription	Gastric	stomach
6	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:7913200-7918200	Weak transcription	Colonic Mucosa	Colon
10	chr4:7913200-7919400	Weak transcription	Right Atrium	heart
11	chr4:7913200-7919600	Weak transcription	Lung	lung
12	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:7913400-7918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:7913400-7918800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:7913400-7919800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
17	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:7913600-7930400	Weak transcription	NHEK	skin
19	chr4:7913800-7919600	Weak transcription	Adipose Nuclei	Adipose
20	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:7914000-7918400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:7914000-7919200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:7914000-7919400	Weak transcription	Fetal Intestine Small	intestine
24	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:7914200-7918200	Weak transcription	Brain Germinal Matrix	brain
26	chr4:7914200-7918800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:7914200-7919600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:7914200-7919600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle
30	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
31	chr4:7914400-7925600	Weak transcription	HSMM	muscle
32	chr4:7914800-7918600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:7914800-7919200	Weak transcription	NHLF	lung
34	chr4:7914800-7919600	Weak transcription	HMEC	breast
35	chr4:7915000-7918200	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:7915000-7918200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:7915000-7918200	Weak transcription	Fetal Stomach	stomach
38	chr4:7915000-7918200	Weak transcription	HUVEC	blood vessel
39	chr4:7915000-7926000	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:7915000-7928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:7915000-7930400	Weak transcription	Fetal Lung	lung
42	chr4:7915200-7918400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:7916200-7919600	Enhancers	Fetal Heart	heart
44	chr4:7916200-7921200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:7916400-7919400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr4:7917000-7919000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr4:7917000-7919600	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr4:7917000-7919800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr4:7917200-7918400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr4:7917200-7919200	Enhancers	H9 Cell Line	embryonic stem cell

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