Variant report

Variant	rs9684298
Chromosome Location	chr4:57278167-57278168
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	chr4:57277811..57280010-chr4:57300306..57302094,2	MCF-7	breast:
2	chr4:57256866..57258507-chr4:57276793..57279015,2	K562	blood:

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10015221	0.89[JPT][hapmap]
rs10015634	0.89[JPT][hapmap]
rs10031012	0.82[EUR][1000 genomes]
rs10031550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10034154	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10518	0.89[JPT][hapmap]
rs10866433	0.89[JPT][hapmap]
rs11133438	0.80[EUR][1000 genomes]
rs11133439	0.87[CEU][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11724302	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11733474	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12331363	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12331412	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13114104	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13133016	0.89[EUR][1000 genomes]
rs13141793	0.95[CEU][hapmap];0.80[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13147824	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1356788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1401907	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs1401912	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464286	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474178	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17051687	0.89[JPT][hapmap]
rs17086803	0.89[JPT][hapmap]
rs1976815	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1996650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030365	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049087	0.94[JPT][hapmap]
rs2139512	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292985	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs28559894	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2899063	0.85[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796547	0.87[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822003	0.87[CEU][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4073691	0.94[JPT][hapmap]
rs4167	0.85[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4305581	0.94[JPT][hapmap]
rs4865087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865090	0.85[CEU][hapmap]
rs4865100	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865101	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57503982	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59615456	0.81[EUR][1000 genomes]
rs62310633	0.83[EUR][1000 genomes]
rs6554348	0.87[CEU][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap]
rs6554349	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs6554352	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811821	0.89[JPT][hapmap]
rs6812041	0.92[CHB][hapmap];0.92[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6819534	0.94[JPT][hapmap]
rs6826795	0.95[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841016	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6841053	0.83[ASN][1000 genomes]
rs6856845	0.81[EUR][1000 genomes]
rs7657711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7661712	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671868	0.87[MEX][hapmap]
rs7683781	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7692385	1.00[CEU][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs7693137	0.87[CEU][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap]
rs7693683	0.92[EUR][1000 genomes]
rs7700034	0.84[JPT][hapmap]
rs9312674	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9683679	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9993277	0.83[CEU][hapmap]
rs9996593	0.89[JPT][hapmap]
rs9997639	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9684298	PPAT	cis	lymphoblastoid	seeQTL
rs9684298	AASDH	cis	cerebellum	SCAN
rs9684298	USP46	cis	cerebellum	SCAN
rs9684298	PPAT	cis	normal skin	skin_eQTL
rs9684298	AASDH	cis	parietal	SCAN
rs9684298	AASDH	cis	multi-tissue	Pritchard
rs9684298	PPAT	cis	uninvolved skin	skin_eQTL
rs9684298	PPAT	cis	lesional skin	skin_eQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
4	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
7	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
12	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
13	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
16	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:57274200-57296400	Weak transcription	Dnd41	blood
18	chr4:57275000-57278200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:57275000-57278400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:57275400-57278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:57275400-57278200	Enhancers	NHDF-Ad	bronchial
22	chr4:57276200-57280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:57276400-57278600	Active TSS	Brain Angular Gyrus	brain
24	chr4:57276600-57278200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:57276600-57278600	Enhancers	K562	blood
26	chr4:57276800-57278200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:57276800-57284200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:57277000-57278200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr4:57277000-57278400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:57277000-57278600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:57277000-57278800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:57277000-57279400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:57277000-57280200	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:57277000-57280200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:57277000-57280400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:57277000-57287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:57277000-57287200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:57277000-57287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:57277000-57289800	Weak transcription	Fetal Stomach	stomach
40	chr4:57277000-57290000	Weak transcription	Aorta	Aorta
41	chr4:57277000-57290200	Weak transcription	Ovary	ovary
42	chr4:57277000-57290800	Weak transcription	Right Atrium	heart
43	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:57277000-57300000	Weak transcription	HSMM	muscle
46	chr4:57277200-57278200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr4:57277200-57280200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:57277200-57280200	Weak transcription	HMEC	breast
49	chr4:57277200-57280400	Weak transcription	NH-A	brain
50	chr4:57277200-57283000	Weak transcription	Fetal Intestine Small	intestine

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