Variant report

Variant	rs7677994
Chromosome Location	chr4:175303330-175303331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs11725800	0.89[ASN][1000 genomes]
rs11727574	0.90[ASN][1000 genomes]
rs11732436	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11732586	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11735455	0.90[ASN][1000 genomes]
rs11932821	0.81[AFR][1000 genomes]
rs12233848	0.83[ASN][1000 genomes]
rs13101376	0.90[ASN][1000 genomes]
rs13102962	0.90[ASN][1000 genomes]
rs13107351	0.89[ASN][1000 genomes]
rs13108930	0.89[ASN][1000 genomes]
rs13109756	0.90[ASN][1000 genomes]
rs13120534	0.90[ASN][1000 genomes]
rs13122946	0.89[ASN][1000 genomes]
rs13126536	0.88[ASN][1000 genomes]
rs13132617	0.89[ASN][1000 genomes]
rs13135662	0.83[ASN][1000 genomes]
rs13140627	0.89[ASN][1000 genomes]
rs13145787	0.88[ASN][1000 genomes]
rs13146439	0.89[ASN][1000 genomes]
rs13149585	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149810	0.89[ASN][1000 genomes]
rs13150656	0.89[ASN][1000 genomes]
rs13152348	0.80[ASN][1000 genomes]
rs1922383	0.90[ASN][1000 genomes]
rs1922384	0.89[ASN][1000 genomes]
rs28519075	0.90[ASN][1000 genomes]
rs28657489	0.89[ASN][1000 genomes]
rs34037587	0.89[ASN][1000 genomes]
rs34054930	0.85[ASN][1000 genomes]
rs34135350	0.85[ASN][1000 genomes]
rs34175211	0.86[ASN][1000 genomes]
rs34400328	0.92[ASN][1000 genomes]
rs34421418	0.91[ASN][1000 genomes]
rs34425026	0.92[ASN][1000 genomes]
rs34572193	0.88[ASN][1000 genomes]
rs34592304	0.85[ASN][1000 genomes]
rs34604934	0.89[ASN][1000 genomes]
rs34609084	0.89[ASN][1000 genomes]
rs34674779	0.80[ASN][1000 genomes]
rs34717346	0.91[ASN][1000 genomes]
rs34795808	0.90[ASN][1000 genomes]
rs34833822	0.88[ASN][1000 genomes]
rs35078417	0.90[ASN][1000 genomes]
rs35211627	0.84[ASN][1000 genomes]
rs35263478	0.89[ASN][1000 genomes]
rs35295528	0.88[ASN][1000 genomes]
rs35326753	0.83[ASN][1000 genomes]
rs35347093	0.90[ASN][1000 genomes]
rs35423027	0.86[ASN][1000 genomes]
rs35539859	0.87[ASN][1000 genomes]
rs35635103	0.92[ASN][1000 genomes]
rs35663303	0.88[ASN][1000 genomes]
rs35697391	0.91[ASN][1000 genomes]
rs35706347	0.80[ASN][1000 genomes]
rs35760448	0.90[ASN][1000 genomes]
rs35794791	0.82[ASN][1000 genomes]
rs35920928	0.89[ASN][1000 genomes]
rs35931018	0.82[ASN][1000 genomes]
rs35978128	0.89[ASN][1000 genomes]
rs36122870	0.89[ASN][1000 genomes]
rs3980460	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131102	0.91[ASN][1000 genomes]
rs4131103	0.90[ASN][1000 genomes]
rs4273447	0.90[ASN][1000 genomes]
rs4518223	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4518224	0.86[ASN][1000 genomes]
rs4568217	0.90[ASN][1000 genomes]
rs4695776	0.91[ASN][1000 genomes]
rs4695929	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335849	0.91[ASN][1000 genomes]
rs62335856	0.91[ASN][1000 genomes]
rs62335857	0.92[ASN][1000 genomes]
rs62337061	0.90[ASN][1000 genomes]
rs62337062	0.90[ASN][1000 genomes]
rs62337063	0.90[ASN][1000 genomes]
rs62337086	0.89[ASN][1000 genomes]
rs62337087	0.89[ASN][1000 genomes]
rs6553785	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6553786	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6553789	0.90[ASN][1000 genomes]
rs6553790	0.90[ASN][1000 genomes]
rs6553791	0.90[ASN][1000 genomes]
rs67728476	0.90[ASN][1000 genomes]
rs6812366	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822535	0.87[ASN][1000 genomes]
rs6827853	0.88[ASN][1000 genomes]
rs6835446	0.92[ASN][1000 genomes]
rs6852435	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6853004	0.90[ASN][1000 genomes]
rs6853166	0.90[ASN][1000 genomes]
rs6853181	0.90[ASN][1000 genomes]
rs7654427	0.90[ASN][1000 genomes]
rs7655606	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7656628	0.92[ASN][1000 genomes]
rs7665426	0.89[ASN][1000 genomes]
rs7665708	0.90[ASN][1000 genomes]
rs7667325	0.90[ASN][1000 genomes]
rs7667374	0.90[ASN][1000 genomes]
rs7667642	0.90[ASN][1000 genomes]
rs7671492	0.92[ASN][1000 genomes]
rs7672838	0.90[ASN][1000 genomes]
rs7680564	0.90[ASN][1000 genomes]
rs7687802	0.90[ASN][1000 genomes]
rs7688229	0.87[ASN][1000 genomes]
rs7689422	0.90[ASN][1000 genomes]
rs7689484	0.91[ASN][1000 genomes]
rs7691061	0.90[ASN][1000 genomes]
rs7695912	0.90[ASN][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	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	esv3356953	chr4:175301838-175304939	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7677994	KIAA1712	cis	parietal	SCAN
rs7677994	VEGFC	cis	parietal	SCAN
rs7677994	NXF1	trans	parietal	SCAN
rs7677994	FBXO8	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175297000-175304400	Weak transcription	K562	blood
2	chr4:175297400-175304800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:175300400-175303400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:175300600-175303600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr4:175300600-175305000	Weak transcription	A549	lung
6	chr4:175301200-175305000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:175301400-175303600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr4:175301800-175303400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:175301800-175303600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:175301800-175310600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:175302200-175305000	Weak transcription	Placenta	Placenta
12	chr4:175302400-175305000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr4:175302800-175305000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:175303200-175304200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:175303200-175304400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:175303200-175304400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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