Variant report

Variant	rs1807355
Chromosome Location	chr12:10163072-10163073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:10162940-10163090	HEEpiC	esophagus:	n/a	n/a
2	CTCF	chr12:10162960-10163110	HRE	kidney:	n/a	n/a
3	CTCF	chr12:10162940-10163090	HPF	lung:	n/a	n/a
4	CHD1	chr12:10163016-10163077	GM12878	blood:	n/a	n/a
5	CTCF	chr12:10162940-10163090	Caco-2	colon:	n/a	n/a
6	CTCF	chr12:10163040-10163190	HepG2	liver:	n/a	n/a
7	CTCF	chr12:10163020-10163170	BE2_C	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:10163030-10163080	AG04449	skin:	fetal
2	chr12:10163030-10163080	LNCaP	prostate:	n/a
3	chr12:10163030-10163080	Hela-S3	cervix:	n/a
4	chr12:10163030-10163080	HRE	kidney:	n/a
5	chr12:10163030-10163080	Caco-2	colon:	n/a
6	chr12:10163030-10163080	HIPEpiC	eye:	n/a
7	chr12:10163030-10163080	AG04450	lung:	fetal
8	chr12:10163030-10163080	NHDF-neo	bronchial:	n/a
9	chr12:10163030-10163080	GM19239	blood:	n/a
10	chr12:10163030-10163080	T-47D	breast:	n/a
11	chr12:10163030-10163080	SKMC	muscle:	n/a
12	chr12:10163030-10163080	H1-hESC	embryonic stem cell:	embryo
13	chr12:10163030-10163080	CMK	blood:	n/a
14	chr12:10163030-10163080	GM12891	blood:	n/a
15	chr12:10163030-10163080	PFSK-1	brain:	n/a
16	chr12:10163030-10163080	RPTEC	kidney:	n/a
17	chr12:10163030-10163080	SK-N-SH_RA	brain:	n/a
18	chr12:10163030-10163080	NB4	blood:	n/a
19	chr12:10163030-10163080	HUVEC	blood vessel:	n/a
20	chr12:10163030-10163080	ProgFib	skin:	n/a
21	chr12:10163030-10163080	IMR90	lung:	fetal
22	chr12:10163030-10163080	HNPCEpiC	eye:	n/a
23	chr12:10163030-10163080	HMEC	breast:	n/a
24	chr12:10163030-10163080	SAEC	small airway:	n/a
25	chr12:10163030-10163080	MCF-7	breast:	n/a
26	chr12:10163030-10163080	K562	blood:	n/a
27	chr12:10163030-10163080	HCM	heart:	n/a
28	chr12:10163030-10163080	SK-N-SH	brain:	n/a
29	chr12:10163030-10163080	HAEpiC	amniotic membrane:	n/a
30	chr12:10163030-10163080	HEEpiC	esophagus:	n/a
31	chr12:10163030-10163080	MCF10A-Er-Src	breast:	n/a
32	chr12:10163030-10163080	GM06990	blood:	n/a
33	chr12:10163030-10163080	HPAEpiC	pulmonary alveolar:	n/a
34	chr12:10163030-10163080	ECC-1	luminal epithelium:	n/a
35	chr12:10163030-10163080	HCPEpiC	choroid plexus:	n/a
36	chr12:10163030-10163080	HCT-116	colon:	n/a
37	chr12:10163030-10163080	BE2_C	brain:	n/a
38	chr12:10163030-10163080	SK-N-MC	brain:	n/a
39	chr12:10163030-10163080	BJ	skin:	n/a
40	chr12:10163030-10163080	ovcar-3	ovarian:	n/a
41	chr12:10163030-10163080	AG10803	skin:	n/a
42	chr12:10163030-10163080	NHBE	bronchial:	n/a
43	chr12:10163030-10163080	AoSMC	blood vessel:	n/a
44	chr12:10163030-10163080	NT2-D1	testis:	n/a
45	chr12:10163030-10163080	HRCEpiC	kidney:	n/a
46	chr12:10163030-10163080	Hepatocyte	liver:	n/a
47	chr12:10163030-10163080	Jurkat	blood:	n/a
48	chr12:10163030-10163080	GM12878	blood:	n/a
49	chr12:10163030-10163080	PrEC	prostate:	n/a
50	chr12:10163030-10163080	GM12892	blood:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10162252..10163209-chr12:10292996..10293711,2	MCF-7	breast:
2	chr12:9966874..9967473-chr12:10162556..10163093,2	MCF-7	breast:

No data

Variant related genes	Relation type
CLEC12B	TF binding region
CLEC12B	CpG island

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10400513	0.87[EUR][1000 genomes]
rs10400556	0.85[EUR][1000 genomes]
rs10400564	0.86[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10400568	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs10466840	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1054611	0.84[JPT][hapmap]
rs1075996	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772225	0.93[EUR][1000 genomes]
rs1359082	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868211	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868212	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4764177	0.81[TSI][hapmap]
rs4764182	0.88[ASN][1000 genomes]
rs4764183	0.88[ASN][1000 genomes]
rs4764184	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4764185	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4764186	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4764187	0.81[CEU][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4764188	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs620449	0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7134176	0.97[ASN][1000 genomes]
rs7134681	0.97[ASN][1000 genomes]
rs7305054	0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7305223	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7954941	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7957224	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7960084	0.86[CEU][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7960202	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970682	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9300223	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3429200	chr12:10162800-10163075	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1807355	ACRBP	cis	parietal	SCAN
rs1807355	PRH2	cis	parietal	SCAN
rs1807355	GABARAPL1	cis	cerebellum	SCAN
rs1807355	SCARNA10	cis	cerebellum	SCAN
rs1807355	ATN1	cis	cerebellum	SCAN
rs1807355	SCARNA12	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10156200-10165200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:10159200-10163200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:10162400-10163200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:10162400-10163800	Enhancers	HUVEC	blood vessel
5	chr12:10162800-10163200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:10162800-10163600	Enhancers	Brain Substantia Nigra	brain
7	chr12:10163000-10163200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:10163000-10163200	Enhancers	Brain Hippocampus Middle	brain
9	chr12:10163000-10163600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:10163000-10163800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:10163000-10165400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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