Variant report

Variant	rs4339829
Chromosome Location	chr1:227478028-227478029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227472633..227474570-chr1:227477067..227478764,2	K562	blood:
2	chr1:227472840..227475102-chr1:227475698..227478764,3	K562	blood:
3	chr1:227477234..227482232-chr1:227484947..227488828,5	K562	blood:
4	chr1:227477181..227481565-chr1:227505488..227508633,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10429872	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10495255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10737428	0.90[ASN][1000 genomes]
rs10753433	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10799409	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799410	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916106	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916108	0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916111	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916118	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916122	0.90[ASN][1000 genomes]
rs12035986	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12044287	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12065126	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125514	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs12137591	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12565056	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs12565871	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12566059	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12569227	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1304324	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2102638	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2953638	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs2953652	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2953655	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014252	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014253	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3014256	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs3014267	0.83[JPT][hapmap]
rs34084723	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34875093	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35738984	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3795457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653797	0.84[AMR][1000 genomes]
rs4653812	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653823	0.88[ASN][1000 genomes]
rs4653824	0.89[ASN][1000 genomes]
rs4653825	0.88[ASN][1000 genomes]
rs60197034	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656653	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682120	0.90[ASN][1000 genomes]
rs6684784	0.90[ASN][1000 genomes]
rs6684803	0.90[ASN][1000 genomes]
rs6685106	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6692294	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6697272	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6700730	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72759337	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516326	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519752	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955704	0.91[CEU][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3453491	chr1:227462942-227482283	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3453492	chr1:227462956-227482280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4339829	DNAH14	cis	parietal	SCAN
rs4339829	PRSS38	cis	parietal	SCAN
rs4339829	PARP1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
2	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:227467200-227485800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:227469200-227500200	Weak transcription	Left Ventricle	heart
5	chr1:227469200-227502600	Weak transcription	HSMM	muscle
6	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
7	chr1:227470600-227483000	Weak transcription	Stomach Mucosa	stomach
8	chr1:227470600-227485800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:227473800-227486200	Weak transcription	Aorta	Aorta
10	chr1:227474000-227478200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:227474200-227486200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:227474600-227486000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:227474800-227485800	Weak transcription	HUVEC	blood vessel
14	chr1:227474800-227486200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:227474800-227486200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:227475000-227484200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:227475000-227486200	Weak transcription	HMEC	breast
18	chr1:227475000-227491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:227475200-227500200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:227475800-227484800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:227475800-227485200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:227475800-227486400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:227476000-227479200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:227476200-227486200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:227477000-227486200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:227477200-227485000	Weak transcription	K562	blood
28	chr1:227478000-227491800	Weak transcription	Psoas Muscle	Psoas

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