Variant report

Variant	rs675065
Chromosome Location	chr1:212634583-212634584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212634490..212636091-chr1:212645524..212647172,2	K562	blood:
2	chr1:212632904..212637583-chr1:212637604..212642982,9	K562	blood:
3	chr1:212626698..212637479-chr1:212779685..212784714,19	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000224535	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10863967	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10863968	0.99[ASN][1000 genomes]
rs10863969	0.85[CEU][hapmap]
rs11119937	0.92[ASN][1000 genomes]
rs11119940	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11119941	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11119943	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11119944	1.00[ASN][1000 genomes]
rs12023863	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17019129	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3767870	0.80[JPT][hapmap]
rs3767872	0.90[ASN][1000 genomes]
rs4951446	0.94[ASN][1000 genomes]
rs4951447	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4951448	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs4951598	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4951599	1.00[ASN][1000 genomes]
rs4951600	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59001230	0.94[ASN][1000 genomes]
rs731075	0.87[CEU][hapmap]
rs791720	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873157	chr1:212610755-212640982	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv873158	chr1:212610755-212646225	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv873163	chr1:212629935-212669475	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv524329	chr1:212631393-212634583	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv519924	chr1:212631393-212638725	Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs675065	CR1L	cis	parietal	SCAN
rs675065	PIGR	cis	cerebellum	SCAN
rs675065	LQK1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212614400-212636800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:212619600-212636800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:212629800-212640000	Weak transcription	Pancreas	Pancrea
4	chr1:212629800-212642600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:212629800-212643200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:212632000-212635200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:212632000-212636400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:212632200-212636400	Enhancers	Brain Angular Gyrus	brain
9	chr1:212632200-212637400	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:212632200-212637400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:212632800-212637000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:212633400-212637000	Enhancers	Brain Anterior Caudate	brain
13	chr1:212633600-212634800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:212634200-212636800	Enhancers	Brain Substantia Nigra	brain
15	chr1:212634200-212637600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:212634400-212637000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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