Variant report

Variant	rs13127935
Chromosome Location	chr4:7913961-7913962
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	chr4:7913036..7915601-chr4:7939958..7942637,2	MCF-7	breast:
2	chr4:7913753..7915419-chr4:7919599..7921984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10938695	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12641498	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs13115283	0.94[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs13139805	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1320074	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs1320075	0.84[EUR][1000 genomes]
rs16841407	0.84[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17770447	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17833038	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1878325	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2385910	0.83[EUR][1000 genomes]
rs28500712	0.84[ASN][1000 genomes]
rs28681260	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34179701	0.85[EUR][1000 genomes]
rs4447866	0.83[CHB][hapmap]
rs4549363	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4696746	0.84[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	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6811851	0.83[EUR][1000 genomes]
rs6824410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824700	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6831381	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs6839119	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]
rs6844956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845653	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6846317	0.85[EUR][1000 genomes]
rs6848540	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6857814	0.83[EUR][1000 genomes]
rs7694650	0.84[EUR][1000 genomes]
rs938604	0.84[CEU][hapmap];0.84[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
rs13127935	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:81 , 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	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
4	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
5	chr4:7906000-7914200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:7906200-7914400	Enhancers	HUVEC	blood vessel
7	chr4:7907800-7914200	Enhancers	Brain Germinal Matrix	brain
8	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
9	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
10	chr4:7910800-7914200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:7911000-7914000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr4:7911000-7914200	Enhancers	HMEC	breast
13	chr4:7911200-7914000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:7911200-7914000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:7911200-7914000	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr4:7911200-7914400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:7911200-7917000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:7911400-7914000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr4:7911400-7914000	Enhancers	Brain Hippocampus Middle	brain
20	chr4:7911400-7914000	Enhancers	Fetal Brain Male	brain
21	chr4:7911400-7914400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr4:7911400-7917400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:7911600-7914000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:7912000-7918000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
26	chr4:7912400-7914000	Enhancers	Fetal Intestine Small	intestine
27	chr4:7912600-7914600	Weak transcription	HepG2	liver
28	chr4:7912600-7917000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:7912600-7917200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:7912800-7914200	Enhancers	Fetal Kidney	kidney
31	chr4:7912800-7914200	Enhancers	HSMMtube	muscle
32	chr4:7912800-7931200	Weak transcription	Gastric	stomach
33	chr4:7913000-7914200	Enhancers	NH-A	brain
34	chr4:7913000-7914800	Enhancers	NHLF	lung
35	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
38	chr4:7913200-7914000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:7913200-7914000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:7913200-7914000	Weak transcription	Placenta	Placenta
41	chr4:7913200-7914400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr4:7913200-7914800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:7913200-7917400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:7913200-7918200	Weak transcription	Colonic Mucosa	Colon
45	chr4:7913200-7919400	Weak transcription	Right Atrium	heart
46	chr4:7913200-7919600	Weak transcription	Lung	lung
47	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:7913400-7914000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:7913400-7914200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr4:7913400-7914200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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