Variant report

Variant	rs3746003
Chromosome Location	chr19:44130453-44130454
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	POLR2A	chr19:44129782-44130581	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr19:44130320-44130470	GM12875	blood:	n/a	n/a
3	CTCF	chr19:44130409-44130484	GM20000	blood:	n/a	n/a
4	EGR1	chr19:44130309-44130632	K562	blood:	n/a	chr19:44130486-44130501
5	RCOR1	chr19:44130390-44130544	K562	blood:	n/a	n/a
6	HMGN3	chr19:44130008-44130503	K562	blood:	n/a	n/a
7	CTCF	chr19:44130290-44130581	K562	blood:	n/a	n/a
8	CTCF	chr19:44130380-44130489	A549	lung:	n/a	n/a
9	CTCF	chr19:44130357-44130523	MCF-7	breast:	n/a	n/a
10	CTCF	chr19:44130340-44130490	HCPEpiC	choroid plexus:	n/a	n/a
11	CBX3	chr19:44130178-44130735	K562	blood:	n/a	n/a
12	USF1	chr19:44130367-44130790	ECC-1	luminal epithelium:	n/a	n/a
13	SMC3	chr19:44130367-44130523	K562	blood:	n/a	n/a
14	MYC	chr19:44130296-44130709	K562	blood:	n/a	chr19:44130597-44130604 chr19:44130596-44130605 chr19:44130595-44130605 chr19:44130595-44130606
15	POLR2A	chr19:44130024-44130553	HepG2	liver:	n/a	n/a
16	CTCF	chr19:44130291-44130570	A549	lung:	n/a	n/a
17	TBP	chr19:44130327-44130548	K562	blood:	n/a	n/a
18	CTCF	chr19:44130399-44130507	MCF-7	breast:	n/a	n/a
19	E2F6	chr19:44130446-44130667	K562	blood:	n/a	n/a
20	JUN	chr19:44130447-44130663	K562	blood:	n/a	n/a
21	EGR1	chr19:44130293-44130695	K562	blood:	n/a	chr19:44130486-44130501
22	CTCF	chr19:44130247-44130563	K562	blood:	n/a	n/a
23	CTCF	chr19:44130400-44130550	HBMEC	blood vessel:	n/a	n/a
24	BHLHE40	chr19:44130251-44130746	K562	blood:	n/a	n/a
25	JUND	chr19:44130336-44130498	K562	blood:	n/a	n/a
26	USF1	chr19:44130395-44130772	ECC-1	luminal epithelium:	n/a	n/a
27	MAZ	chr19:44130267-44130656	K562	blood:	n/a	chr19:44130597-44130604 chr19:44130596-44130605 chr19:44130595-44130605 chr19:44130595-44130606
28	CTCF	chr19:44130320-44130470	HMF	breast:	n/a	n/a
29	CTCF	chr19:44130380-44130530	HRPEpiC	eye:	n/a	n/a
30	POLR2A	chr19:44130359-44130597	K562	blood:	n/a	n/a
31	MAX	chr19:44130263-44130794	K562	blood:	n/a	chr19:44130597-44130604 chr19:44130596-44130605 chr19:44130595-44130605 chr19:44130595-44130606
32	CTCF	chr19:44130200-44130490	HVMF	connective:	n/a	n/a
33	CTCF	chr19:44130360-44130510	HPF	lung:	n/a	n/a
34	CTCF	chr19:44130340-44130490	BE2_C	brain:	n/a	n/a
35	CTCF	chr19:44130360-44130510	K562	blood:	n/a	n/a
36	ELF1	chr19:44130342-44130577	K562	blood:	n/a	n/a
37	CTCF	chr19:44130184-44130616	K562	blood:	n/a	n/a
38	CTCF	chr19:44130394-44130496	GM13977	blood:	n/a	n/a
39	NFIC	chr19:44130222-44130742	ECC-1	luminal epithelium:	n/a	chr19:44130516-44130533 chr19:44130517-44130533
40	CTCF	chr19:44130340-44130490	BJ	skin:	n/a	n/a
41	MAX	chr19:44130430-44130728	K562	blood:	n/a	chr19:44130597-44130604 chr19:44130596-44130605 chr19:44130595-44130605 chr19:44130595-44130606
42	CTCF	chr19:44130320-44130470	GM12872	blood:	n/a	n/a
43	CTCF	chr19:44130324-44130564	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr19:44130280-44130630	K562	blood:	n/a	n/a
45	CTCF	chr19:44130340-44130490	GM12865	blood:	n/a	n/a
46	MAX	chr19:44130350-44130734	K562	blood:	n/a	chr19:44130597-44130604 chr19:44130596-44130605 chr19:44130595-44130605 chr19:44130595-44130606
47	USF1	chr19:44130373-44130805	K562	blood:	n/a	n/a
48	MYC	chr19:44130392-44130814	K562	blood:	n/a	chr19:44130597-44130604 chr19:44130596-44130605 chr19:44130595-44130605 chr19:44130595-44130606
49	CTCF	chr19:44130337-44130549	K562	blood:	n/a	n/a
50	RCOR1	chr19:44130274-44130659	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44097500..44104541-chr19:44116930..44130620,31	K562	blood:
2	chr19:44097777..44104240-chr19:44121602..44130880,30	K562	blood:
3	chr19:44118551..44131201-chr19:44135615..44147023,20	K562	blood:

Variant related genes	Relation type
CADM4	TF binding region
ENSG00000105767	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10408322	0.81[ASN][1000 genomes]
rs11083712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671645	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12461175	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402325	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1402326	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17655574	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1879387	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2003098	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2079646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2302421	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3213266	0.81[LWK][hapmap]
rs3746002	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815422	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803643	0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803644	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73038867	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038875	0.86[ASN][1000 genomes]
rs767540	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs880108	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs939461	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3746003	PRRG2	cis	cerebellum	SCAN
rs3746003	ZNF480	cis	parietal	SCAN
rs3746003	ZNF615	cis	cerebellum	SCAN
rs3746003	IZUMO2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44124600-44143400	Weak transcription	Right Atrium	heart
2	chr19:44124800-44131200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr19:44124800-44138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr19:44124800-44138800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:44124800-44139000	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:44125000-44130800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr19:44125000-44131000	Weak transcription	Fetal Muscle Leg	muscle
8	chr19:44125000-44139200	Weak transcription	Pancreas	Pancrea
9	chr19:44125200-44133000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:44125200-44137400	Weak transcription	HepG2	liver
11	chr19:44125600-44133200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:44125800-44132000	Strong transcription	Fetal Brain Female	brain
13	chr19:44125800-44135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:44126000-44133400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:44126200-44131600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:44126600-44132000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:44126600-44134000	Strong transcription	Brain Germinal Matrix	brain
18	chr19:44126800-44131800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:44127000-44131400	Strong transcription	Fetal Stomach	stomach
20	chr19:44127200-44131400	Strong transcription	Fetal Intestine Small	intestine
21	chr19:44127200-44131800	Strong transcription	Brain Anterior Caudate	brain
22	chr19:44127200-44132000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:44127400-44131000	Strong transcription	Brain Angular Gyrus	brain
24	chr19:44127400-44131000	Strong transcription	Brain Cingulate Gyrus	brain
25	chr19:44127400-44131000	Strong transcription	Brain Hippocampus Middle	brain
26	chr19:44128600-44138800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:44128800-44130600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr19:44128800-44131000	Enhancers	Primary hematopoietic stem cells	blood
29	chr19:44129000-44138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:44129200-44138200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:44129400-44131000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:44129600-44130600	Enhancers	K562	blood
33	chr19:44129600-44131400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:44129800-44131000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:44129800-44131200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr19:44129800-44131600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:44130000-44131400	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr19:44130000-44131400	Bivalent Enhancer	Placenta	Placenta
39	chr19:44130200-44131200	Enhancers	Esophagus	oesophagus
40	chr19:44130200-44131200	Enhancers	Lung	lung
41	chr19:44130200-44131200	Enhancers	Spleen	Spleen
42	chr19:44130200-44131400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:44130200-44131400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr19:44130200-44131800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:44130200-44131800	Genic enhancers	Brain Substantia Nigra	brain
46	chr19:44130400-44130600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
47	chr19:44130400-44130600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
48	chr19:44130400-44130600	Bivalent Enhancer	Thymus	Thymus
49	chr19:44130400-44130800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:44130400-44131200	Enhancers	Gastric	stomach

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