Variant report

Variant	rs1194607
Chromosome Location	chr1:154294656-154294657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:154294471-154294828	K562	blood:	n/a	chr1:154294561-154294576 chr1:154294563-154294572 chr1:154294559-154294574 chr1:154294562-154294573 chr1:154294564-154294571
2	MAX	chr1:154294491-154294694	K562	blood:	n/a	chr1:154294561-154294576 chr1:154294563-154294572 chr1:154294559-154294574 chr1:154294562-154294573 chr1:154294564-154294571
3	RCOR1	chr1:154294562-154294657	K562	blood:	n/a	n/a
4	MAX	chr1:154294538-154294670	K562	blood:	n/a	chr1:154294561-154294576 chr1:154294563-154294572 chr1:154294559-154294574 chr1:154294562-154294573 chr1:154294564-154294571

No.	Distal block	Cell Line	Cell type
1	chr1:154154218..154156961-chr1:154294191..154296941,2	MCF-7	breast:
2	chr1:154293042..154295327-chr1:154297413..154299149,2	MCF-7	breast:
3	chr1:154243817..154246754-chr1:154291993..154294660,2	K562	blood:
4	chr1:154192079..154194850-chr1:154292071..154294843,2	K562	blood:

Variant related genes	Relation type
ATP8B2	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10908831	0.86[ASN][1000 genomes]
rs11265604	0.86[JPT][hapmap]
rs11578607	0.88[EUR][1000 genomes]
rs11581043	0.89[EUR][1000 genomes]
rs1194584	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1194585	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194586	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194587	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194592	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1194608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033720	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12121085	0.92[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap]
rs1685606	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1760794	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1760795	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17654071	0.90[CHD][hapmap];0.84[GIH][hapmap]
rs2483712	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2633433	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28409746	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34870927	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4103781	0.88[EUR][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv946406	chr1:154284237-154294738	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1194607	LCE1C	cis	cerebellum	SCAN
rs1194607	THEM4	cis	parietal	SCAN
rs1194607	S100A4	cis	parietal	SCAN
rs1194607	VHLL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154290400-154297000	Weak transcription	Thymus	Thymus
2	chr1:154293000-154294800	Enhancers	Fetal Intestine Large	intestine
3	chr1:154293200-154294800	Enhancers	Duodenum Mucosa	Duodenum
4	chr1:154293600-154297000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:154293600-154297200	Weak transcription	Gastric	stomach
6	chr1:154293800-154296800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:154293800-154296800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:154293800-154297000	Weak transcription	Right Ventricle	heart
9	chr1:154293800-154297000	Weak transcription	Spleen	Spleen
10	chr1:154293800-154297200	Weak transcription	Left Ventricle	heart
11	chr1:154293800-154297200	Weak transcription	Pancreas	Pancrea
12	chr1:154293800-154297200	Weak transcription	Right Atrium	heart
13	chr1:154294000-154296800	Weak transcription	Fetal Heart	heart
14	chr1:154294200-154295400	Flanking Active TSS	K562	blood
15	chr1:154294400-154294800	Enhancers	Fetal Intestine Small	intestine
16	chr1:154294400-154296600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:154294600-154294800	Bivalent Enhancer	HepG2	liver
18	chr1:154294600-154296600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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