Variant report

Variant	rs270707
Chromosome Location	chr1:45049458-45049459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45045070..45047329-chr1:45047973..45050362,2	K562	blood:
2	chr1:45045070..45047469-chr1:45047973..45050744,2	K562	blood:
3	chr1:45041622..45043509-chr1:45047717..45049476,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf228-4	chr1:45047311-45049479	ucscGeneNc_uc001cmr_1

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10890309	0.90[CEU][hapmap];0.84[CHB][hapmap];0.87[EUR][1000 genomes]
rs156651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156652	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270703	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs270706	0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs270708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270709	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270710	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270711	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270713	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs270714	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs270716	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs270719	0.95[ASN][1000 genomes]
rs270760	0.89[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs270761	0.87[EUR][1000 genomes]
rs275075	0.92[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs275079	0.99[ASN][1000 genomes]
rs6429543	0.98[ASN][1000 genomes]
rs69141	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs270707	ZNF642	cis	parietal	SCAN
rs270707	GPBP1L1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45018000-45082600	Weak transcription	Right Atrium	heart
2	chr1:45042200-45050600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45042400-45051000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:45043200-45051600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:45046600-45050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:45046600-45054800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:45046800-45053600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:45047000-45050800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:45047400-45049600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:45047800-45060000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:45048200-45053400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:45048600-45050200	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:45048600-45052000	Enhancers	Brain Hippocampus Middle	brain
14	chr1:45048800-45053000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr1:45049000-45052600	Enhancers	Brain Substantia Nigra	brain
16	chr1:45049000-45062800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr1:45049200-45050000	Enhancers	Brain Anterior Caudate	brain
18	chr1:45049200-45050800	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:45049200-45051000	Enhancers	Fetal Intestine Large	intestine
20	chr1:45049400-45050200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr1:45049400-45050600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:45049400-45051000	Enhancers	Rectal Mucosa Donor 31	rectum

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