Variant report

Variant	rs7667982
Chromosome Location	chr4:7936522-7936523
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	chr4:7930429..7933293-chr4:7935968..7937557,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10049998	0.86[CHD][hapmap]
rs12641498	0.93[JPT][hapmap]
rs13139805	0.93[JPT][hapmap]
rs1317111	1.00[JPT][hapmap]
rs1320069	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320070	1.00[JPT][hapmap]
rs1320071	1.00[JPT][hapmap]
rs1320074	0.93[JPT][hapmap]
rs13435730	1.00[JPT][hapmap]
rs16841417	1.00[YRI][hapmap]
rs17770447	0.93[JPT][hapmap]
rs17833038	0.93[JPT][hapmap]
rs1814873	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1814874	0.83[EUR][1000 genomes]
rs2385902	0.93[JPT][hapmap]
rs2385911	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385913	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386056	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4235268	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4235269	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4296663	0.81[CHD][hapmap]
rs4345163	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4385040	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696772	0.85[CHD][hapmap]
rs4696778	0.93[JPT][hapmap]
rs4696779	0.93[JPT][hapmap]
rs4696825	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696834	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5012708	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5012709	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447871	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6816560	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819776	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6824266	0.81[CHD][hapmap]
rs6832352	0.81[CHD][hapmap]
rs6848540	0.93[JPT][hapmap]
rs7437940	0.93[JPT][hapmap]
rs7437984	0.93[JPT][hapmap]
rs7655226	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7681378	0.84[ASN][1000 genomes]
rs7683285	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7685634	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7697255	0.81[CHD][hapmap]
rs938604	0.93[JPT][hapmap]

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
rs7667982	AFAP1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:7931400-7939800	Weak transcription	Fetal Kidney	kidney
3	chr4:7931600-7939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:7931600-7939600	Weak transcription	Ovary	ovary
5	chr4:7931600-7939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:7931600-7939800	Weak transcription	Lung	lung
7	chr4:7931800-7937200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:7931800-7937600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:7931800-7938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:7931800-7938600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:7931800-7939600	Weak transcription	Brain Angular Gyrus	brain
12	chr4:7932000-7937400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:7932000-7938000	Weak transcription	Brain Germinal Matrix	brain
14	chr4:7932000-7938800	Weak transcription	Fetal Lung	lung
15	chr4:7932000-7939600	Weak transcription	Brain Anterior Caudate	brain
16	chr4:7932000-7939600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:7932000-7939600	Weak transcription	Left Ventricle	heart
18	chr4:7932000-7939600	Weak transcription	NHLF	lung
19	chr4:7932000-7939800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:7932000-7939800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:7932000-7939800	Weak transcription	Small Intestine	intestine
22	chr4:7932200-7938400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:7932200-7939600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:7932200-7939600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:7932200-7939800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:7932200-7939800	Weak transcription	Pancreas	Pancrea
27	chr4:7932400-7936600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:7932400-7937200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:7932400-7937400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:7932400-7939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:7932600-7937400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:7932800-7939600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:7934400-7936600	Strong transcription	Fetal Intestine Large	intestine
34	chr4:7935400-7936600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:7935400-7936600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:7935400-7936600	Enhancers	HMEC	breast
37	chr4:7935400-7936600	Genic enhancers	HSMM	muscle
38	chr4:7935400-7939600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:7935600-7936600	Enhancers	Gastric	stomach
40	chr4:7935600-7936600	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr4:7935600-7939600	Weak transcription	Aorta	Aorta
42	chr4:7935600-7939600	Enhancers	HSMMtube	muscle
43	chr4:7935800-7936600	Enhancers	Hela-S3	cervix
44	chr4:7935800-7936800	Genic enhancers	A549	lung
45	chr4:7935800-7936800	Enhancers	NHDF-Ad	bronchial
46	chr4:7935800-7937000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:7935800-7938000	Enhancers	Fetal Brain Female	brain
48	chr4:7935800-7938800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:7935800-7939000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:7935800-7939600	Weak transcription	Placenta	Placenta

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