Variant report

Variant	rs974334
Chromosome Location	chr6:28474218-28474219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28457441..28459439-chr6:28472256..28474388,2	K562	blood:
2	chr6:28457939..28459727-chr6:28472888..28474894,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1003359	0.85[ASN][1000 genomes]
rs12661782	0.83[CHD][hapmap]
rs16894139	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2021745	0.84[CHD][hapmap]
rs2071966	0.83[CHD][hapmap]
rs2078035	0.92[ASN][1000 genomes]
rs2078439	0.92[ASN][1000 genomes]
rs2191037	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227228	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[ASN][1000 genomes]
rs2531813	0.84[CHD][hapmap]
rs2531814	0.80[CHD][hapmap]
rs2531822	0.88[ASN][1000 genomes]
rs2859355	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[ASN][1000 genomes]
rs2859356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859372	0.84[CHD][hapmap]
rs2859374	0.81[CHD][hapmap]
rs377514	0.92[ASN][1000 genomes]
rs380879	0.88[ASN][1000 genomes]
rs406113	0.89[ASN][1000 genomes]
rs434112	0.89[ASN][1000 genomes]
rs440481	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs445870	0.85[ASN][1000 genomes]
rs448450	0.88[ASN][1000 genomes]
rs451774	0.89[ASN][1000 genomes]
rs4713167	0.85[ASN][1000 genomes]
rs6456822	0.85[ASN][1000 genomes]
rs6456823	0.85[ASN][1000 genomes]
rs6921021	0.93[ASN][1000 genomes]
rs7743046	0.85[ASN][1000 genomes]
rs7759252	0.86[ASN][1000 genomes]
rs9468385	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs974334	ZNF323	cis	cerebellum	SCAN
rs974334	BTN2A3	cis	cerebellum	SCAN
rs974334	ZSCAN16	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28471200-28474400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28473000-28475000	Enhancers	K562	blood
3	chr6:28473400-28474400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:28473800-28474800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:28473800-28475000	Enhancers	Primary T cells from cord blood	blood
6	chr6:28473800-28475600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:28474000-28474400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:28474000-28475000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr6:28474000-28475000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:28474000-28475200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:28474000-28475400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:28474000-28475400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:28474000-28475600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:28474000-28475800	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:28474000-28475800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:28474000-28475800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:28474200-28475200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:28474200-28475400	Enhancers	HUES48 Cell Line	embryonic stem cell

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