Variant report

Variant	rs226379
Chromosome Location	chr12:9268585-9268586
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	MAFF	chr12:9268330-9268870	HepG2	liver:	n/a	n/a
2	CEBPD	chr12:9268305-9268662	HepG2	liver:	n/a	n/a
3	HDAC2	chr12:9268360-9268858	HepG2	liver:	n/a	n/a
4	REST	chr12:9268395-9268636	HepG2	liver:	n/a	n/a
5	HEY1	chr12:9267413-9269213	HepG2	liver:	n/a	n/a
6	RAD21	chr12:9268334-9268816	HepG2	liver:	n/a	n/a
7	MXI1	chr12:9268288-9268934	HepG2	liver:	n/a	n/a
8	FOXA1	chr12:9268319-9268925	HepG2	liver:	n/a	n/a
9	STAT1	chr12:9268351-9269027	Hela-S3	cervix:	n/a	chr12:9268705-9268716 chr12:9268701-9268721 chr12:9268707-9268715
10	SMC3	chr12:9268273-9269169	HepG2	liver:	n/a	n/a
11	RXRA	chr12:9268346-9268803	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:9268240-9269012	HepG2	liver:	n/a	n/a
13	MYBL2	chr12:9268122-9268974	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:9268285-9268997	HepG2	liver:	n/a	n/a
15	CEBPD	chr12:9268279-9268662	HepG2	liver:	n/a	n/a
16	MBD4	chr12:9267403-9269219	HepG2	liver:	n/a	n/a
17	EP300	chr12:9268256-9268989	HepG2	liver:	n/a	n/a
18	HDAC2	chr12:9268251-9268884	HepG2	liver:	n/a	n/a
19	RAD21	chr12:9268224-9268998	HepG2	liver:	n/a	n/a
20	HNF4A	chr12:9268434-9268751	HepG2	liver:	n/a	n/a
21	RFX5	chr12:9268398-9268929	HepG2	liver:	n/a	n/a
22	FOXA1	chr12:9268200-9268999	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:9267390-9269039	HepG2	liver:	n/a	n/a
24	NFIC	chr12:9267272-9269203	HepG2	liver:	n/a	n/a
25	HEY1	chr12:9267484-9269088	HepG2	liver:	n/a	n/a
26	CTCF	chr12:9268522-9268607	Lung_OC	lung:	n/a	n/a
27	EP300	chr12:9268347-9268873	HepG2	liver:	n/a	n/a
28	TBP	chr12:9268246-9269070	HepG2	liver:	n/a	n/a
29	NR2F2	chr12:9268135-9269068	HepG2	liver:	n/a	n/a
30	JUND	chr12:9268267-9268855	HepG2	liver:	n/a	n/a
31	MAZ	chr12:9268241-9269202	HepG2	liver:	n/a	n/a
32	SIN3AK20	chr12:9268289-9268700	HepG2	liver:	n/a	n/a
33	REST	chr12:9268191-9268883	HepG2	liver:	n/a	n/a
34	TEAD4	chr12:9268235-9269073	HepG2	liver:	n/a	n/a
35	RAD21	chr12:9268249-9268958	HepG2	liver:	n/a	n/a
36	HNF4G	chr12:9268343-9268763	HepG2	liver:	n/a	n/a
37	SRF	chr12:9268490-9268932	HepG2	liver:	n/a	chr12:9268794-9268808 chr12:9268791-9268805 chr12:9268788-9268805 chr12:9268790-9268808 chr12:9268794-9268805 chr12:9268790-9268804
38	POLR2A	chr12:9268293-9268613	HepG2	liver:	n/a	n/a
39	MYBL2	chr12:9268123-9269003	HepG2	liver:	n/a	n/a
40	NFIC	chr12:9268248-9268895	HepG2	liver:	n/a	n/a
41	HNF4A	chr12:9268390-9268759	HepG2	liver:	n/a	n/a
42	REST	chr12:9268415-9268944	H1-neurons	neurons:	n/a	n/a
43	TCF7L2	chr12:9268347-9269268	HepG2	liver:	n/a	n/a
44	SIN3AK20	chr12:9268285-9268702	HepG2	liver:	n/a	n/a
45	RCOR1	chr12:9268352-9268920	HepG2	liver:	n/a	n/a
46	EP300	chr12:9268266-9269072	HepG2	liver:	n/a	n/a
47	POLR2A	chr12:9267422-9269347	HepG2	liver:	n/a	n/a
48	NR2F2	chr12:9268134-9268997	HepG2	liver:	n/a	n/a
49	FOXA1	chr12:9268262-9268897	HepG2	liver:	n/a	n/a
50	EBF1	chr12:9268532-9268808	GM12878	blood:	n/a	chr12:9268679-9268688 chr12:9268678-9268689

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PZP-6	chr12:9268360-9268657	NONHSAT026387
2	lnc-PZP-6	chr12:9268360-9268613	NONHSAT026388

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10743598	0.93[CHD][hapmap]
rs10771307	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10771309	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs10771310	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs10842789	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10842795	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10842820	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10842845	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10842898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11048789	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs113973	0.93[CHD][hapmap]
rs1805651	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1805652	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805653	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805654	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805655	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805656	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805657	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805658	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805659	0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1805660	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805662	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs1805663	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs1805664	0.96[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1805666	0.91[EUR][1000 genomes]
rs1805667	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs1805678	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805681	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2193005	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226380	0.93[CHD][hapmap]
rs226383	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226386	0.93[CHD][hapmap]
rs226388	1.00[CHD][hapmap]
rs226389	0.93[CHD][hapmap]
rs226393	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226395	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226408	0.93[CHD][hapmap]
rs2300147	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2300148	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2377682	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6487574	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6487581	0.92[EUR][1000 genomes]
rs6487585	0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6487587	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs669	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7135781	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7299282	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7299600	0.90[EUR][1000 genomes]
rs7309361	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7310089	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7310167	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7310884	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7310921	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7955940	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs7965184	0.87[EUR][1000 genomes]
rs7968640	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7976461	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs881376	0.96[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.86[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	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	esv3504674	chr12:9243858-9318016	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3502154	chr12:9243906-9317851	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3502155	chr12:9243906-9317851	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3504685	chr12:9243948-9317959	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs226379	CLECL1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9243000-9274800	Weak transcription	Small Intestine	intestine
2	chr12:9246600-9268600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:9249400-9268800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:9250600-9268600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:9252200-9268800	Weak transcription	Primary T cells from cord blood	blood
6	chr12:9262800-9289000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:9264600-9269800	Active TSS	Brain Hippocampus Middle	brain
8	chr12:9264800-9268600	Weak transcription	Primary B cells from cord blood	blood
9	chr12:9264800-9269000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr12:9264800-9270200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr12:9265000-9269000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:9265000-9269200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:9265000-9270000	Active TSS	Right Atrium	heart
14	chr12:9265200-9269200	Active TSS	Duodenum Mucosa	Duodenum
15	chr12:9265200-9269200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr12:9265400-9269000	Active TSS	Fetal Muscle Leg	muscle
17	chr12:9265600-9268600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr12:9265800-9269400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr12:9266000-9269400	Active TSS	Fetal Stomach	stomach
20	chr12:9266000-9269400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:9266200-9268600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:9266200-9268600	Active TSS	Adipose Nuclei	Adipose
23	chr12:9266200-9269000	Active TSS	Fetal Kidney	kidney
24	chr12:9266200-9270800	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:9266200-9274800	Weak transcription	Gastric	stomach
26	chr12:9266400-9269400	Active TSS	Right Ventricle	heart
27	chr12:9266400-9270000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr12:9266400-9270800	Active TSS	Aorta	Aorta
29	chr12:9266800-9269000	Active TSS	Fetal Lung	lung
30	chr12:9267000-9268800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:9267600-9268600	Active TSS	Brain Substantia Nigra	brain
32	chr12:9267600-9268600	Active TSS	Fetal Muscle Trunk	muscle
33	chr12:9267600-9268800	Active TSS	Brain Angular Gyrus	brain
34	chr12:9267600-9268800	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr12:9267600-9269000	Active TSS	Brain Cingulate Gyrus	brain
36	chr12:9267600-9269000	Active TSS	Placenta	Placenta
37	chr12:9267600-9269000	Active TSS	Left Ventricle	heart
38	chr12:9267600-9269000	Active TSS	Rectal Smooth Muscle	rectum
39	chr12:9267600-9269200	Active TSS	Brain Anterior Caudate	brain
40	chr12:9267600-9269200	Active TSS	Colonic Mucosa	Colon
41	chr12:9267600-9269600	Active TSS	Colon Smooth Muscle	Colon
42	chr12:9267800-9269000	Active TSS	Fetal Intestine Small	intestine
43	chr12:9267800-9270200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:9267800-9272200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:9268000-9268600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:9268000-9268800	Active TSS	HepG2	liver
47	chr12:9268000-9270200	Enhancers	Fetal Heart	heart
48	chr12:9268200-9268600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:9268200-9268600	Active TSS	Esophagus	oesophagus
50	chr12:9268200-9268600	Active TSS	Lung	lung

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